[med-svn] [Git][med-team/artemis][master] Fix edam syntax input+output is singular
Andreas Tille
gitlab at salsa.debian.org
Thu Apr 11 20:28:22 BST 2019
Andreas Tille pushed to branch master at Debian Med / artemis
Commits:
bc46cc86 by Andreas Tille at 2019-04-11T19:27:57Z
Fix edam syntax input+output is singular
- - - - -
7 changed files:
- debian/compat
- debian/copyright
- debian/patches/samreader.patch
- debian/patches/series
- debian/patches/use-lang3.patch
- debian/rules
- debian/upstream/edam
Changes:
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-11
+12
=====================================
debian/copyright
=====================================
@@ -1,11 +1,15 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: artemis
Upstream-Contact: <artemis at sanger.ac.uk>
Source: https://github.com/sanger-pathogens/Artemis
Files-Excluded:
lib/*
+ *.jar
test/lib/*
*/jquery.js
+ */*.icns
+ */.*.tmp
+ */.gitignore
Files: *
Copyright: 1998-2013 Genome Research Limited
=====================================
debian/patches/samreader.patch
=====================================
@@ -4,8 +4,8 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
Bug-Debian: https://bugs.debian.org/846671
Last-Update: 2016-12-07 23:37:52 +0000
---- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
-+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+--- a/src/main/java/uk/ac/sanger/artemis/components/alignment/BamUtils.java
++++ b/src/main/java/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -85,14 +85,14 @@ class BamUtils
}
return (float)len;
@@ -32,8 +32,8 @@ Last-Update: 2016-12-07 23:37:52 +0000
int thisStart = start - offset;
if(thisStart < 1)
thisStart = 1;
-@@ -150,7 +150,7 @@ class BamUtils
- {
+@@ -154,7 +154,7 @@ class BamUtils
+ // specifying byStrand as true.
cnt = count(bamView, bam, start, end, contained, true, useStrandTag);
}
-
@@ -41,8 +41,8 @@ Last-Update: 2016-12-07 23:37:52 +0000
float cntf[] = new float[2];
cntf[0] = cnt[0];
cntf[1] = cnt[1];
-@@ -159,7 +159,7 @@ class BamUtils
-
+@@ -178,7 +178,7 @@ class BamUtils
+ */
protected static int[] count(
final BamView bamView,
- final String bam,
@@ -50,31 +50,16 @@ Last-Update: 2016-12-07 23:37:52 +0000
final int start,
final int end,
final boolean contained,
-@@ -197,10 +197,10 @@ class BamUtils
- it.close();
- return cnt;
- }
--
+@@ -234,7 +234,7 @@ class BamUtils
+ * @param progressBar
+ * @return array of mapped read counts
+ */
- protected static int[] calc(
-- final BamView bamView,
-- final String refName,
-+
-+ static int[] calc(
-+ final BamView bamView,
-+ final String refName,
++ static int[] calc(
+ final BamView bamView,
+ final String refName,
final int sequenceLength,
- final boolean useStrandTag,
- final JProgressBar progressBar)
-@@ -240,7 +240,7 @@ class BamUtils
- if (thisEnd > thisLength)
- thisEnd = thisLength;
-
-- mappedReads[j] += BamUtils.count(bamView, bam, thisStart, thisEnd,
-+ mappedReads[j] += BamUtils.count(bamView, bam, thisStart, thisEnd,
- contained, false, useStrandTag)[0];
- }
- lastLen = len;
-@@ -295,7 +295,7 @@ class BamUtils
+@@ -340,7 +340,7 @@ class BamUtils
{
List<AlignmentBlock> blocks = samRecord.getAlignmentBlocks();
boolean isFwd = !samRecord.getReadNegativeStrandFlag();
@@ -83,7 +68,7 @@ Last-Update: 2016-12-07 23:37:52 +0000
for(int j=0; j<blocks.size(); j++)
{
AlignmentBlock block = blocks.get(j);
-@@ -306,12 +306,12 @@ class BamUtils
+@@ -351,12 +351,12 @@ class BamUtils
int bin = pos - start;
if(bin < 0 || bin > cnt.length-1)
continue;
@@ -98,7 +83,7 @@ Last-Update: 2016-12-07 23:37:52 +0000
}
}
}
-@@ -334,13 +334,13 @@ class BamUtils
+@@ -381,13 +381,13 @@ class BamUtils
protected static Hashtable<String, List<ReadCount>> calculateMappedReads(
final BamView bamView,
final FeatureVector features,
@@ -112,2270 +97,5 @@ Last-Update: 2016-12-07 23:37:52 +0000
- final Hashtable<String, List<ReadCount>> featureReadCount =
+ final Hashtable<String, List<ReadCount>> featureReadCount =
new Hashtable<String, List<ReadCount>>();
- for (int i = 0; i < features.size(); i++)
- {
-@@ -381,7 +381,7 @@ class BamUtils
- cnt[1] -= tmpcnt[1];
- }
- }
--
-+
- if (mappedReads != null)
- {
- cnt[0] = (cnt[0] / (((float) mappedReads[j] / 1000000.f) * (fLen / 1000.f)));
---- a/uk/ac/sanger/artemis/components/alignment/BamView.java
-+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
-@@ -186,15 +185,15 @@ public class BamView extends JPanel
- private Bases bases;
- private JScrollPane jspView;
- private JScrollBar scrollBar;
--
-+
- private SequenceComboBox combo;
- private boolean isOrientation = false;
- private boolean isSingle = false;
- private boolean isSNPs = false;
--
-+
- private boolean isCoverage = false;
- private boolean isSNPplot = false;
--
-+
- private EntryEdit entry_edit;
- private FeatureDisplay feature_display;
- private Selection selection;
-@@ -205,7 +204,7 @@ public class BamView extends JPanel
- private boolean logScale = false;
- private Ruler ruler;
- private int nbasesInView;
--
-+
- private int startBase = -1;
- private int endBase = -1;
- private int laststart;
-@@ -304,8 +303,8 @@ public class BamView extends JPanel
- this(bamList, reference, nbasesInView, feature_display, bases, containerPanel, frame);
- this.entry_edit = entry_edit;
- }
--
-- public BamView(List<String> bamList,
-+
-+ public BamView(List<String> bamList,
- String reference,
- int nbasesInView,
- final FeatureDisplay feature_display,
-@@ -407,13 +406,13 @@ public class BamView extends JPanel
-
- final javax.swing.plaf.FontUIResource font_ui_resource =
- Options.getOptions().getFontUIResource();
--
-+
- Enumeration<Object> keys = UIManager.getDefaults().keys();
-- while(keys.hasMoreElements())
-+ while(keys.hasMoreElements())
- {
- Object key = keys.nextElement();
- Object value = UIManager.get(key);
-- if(value instanceof javax.swing.plaf.FontUIResource)
-+ if(value instanceof javax.swing.plaf.FontUIResource)
- UIManager.put(key, font_ui_resource);
- }
-
-@@ -422,10 +421,10 @@ public class BamView extends JPanel
- ALIGNMENT_PIX_PER_BASE = fm.charWidth('M');
- BASE_HEIGHT = fm.getMaxAscent();
- selection = new Selection(null);
--
-+
- MultiLineToolTipUI.initialize();
- setToolTipText("");
--
-+
- buttonGroup.add(cbStackView);
- buttonGroup.add(cbPairedStackView);
- buttonGroup.add(cbStrandStackView);
-@@ -435,10 +434,10 @@ public class BamView extends JPanel
- buttonGroup.add(cbCoverageHeatMap);
- addMouseListener(new PopupListener());
-
-- jspView = new JScrollPane(this,
-+ jspView = new JScrollPane(this,
- JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
- JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
--
-+
- jspView.setViewportBorder(BorderFactory.createMatteBorder(0, 0, 1, 0, Color.DARK_GRAY));
- Border empty = new EmptyBorder(0,0,0,0);
- jspView.setBorder(empty);
-@@ -633,7 +632,7 @@ public class BamView extends JPanel
- return bamIndex;
- }
-
-- public void run()
-+ public void run()
- {
- exception = null;
-
-@@ -699,7 +698,7 @@ public class BamView extends JPanel
- }
- //inputSam.close();
- }
--
-+
- /**
- * Iterate over BAM file and load into the <code>List</code> of
- * <code>SAMRecord</code>.
-@@ -747,7 +746,7 @@ public class BamView extends JPanel
-
- if(readGrpFrame != null && !readGrpFrame.isReadGroupVisible(samRecord.getReadGroup()))
- continue;
--
-+
- if( samRecordFlagPredicate == null ||
- !samRecordFlagPredicate.testPredicate(samRecord))
- {
-@@ -757,7 +756,7 @@ public class BamView extends JPanel
- int abeg = samRecord.getAlignmentStart();
- int aend = samRecord.getAlignmentEnd();
- boolean over = false;
--
-+
- for(int i=abeg; i<aend; i++)
- {
- int bin = ((i-start)/binSize)-1;
-@@ -772,7 +771,7 @@ public class BamView extends JPanel
- break;
- }
- }
--
-+
- if(over)
- continue;
-
-@@ -786,7 +785,7 @@ public class BamView extends JPanel
- readsInView.add(new BamViewRecord(samRecord, bamIndex));
- }
- }
--
-+
- if(cnt > checkMemAfter)
- {
- cnt = 0;
-@@ -794,11 +793,11 @@ public class BamView extends JPanel
- (float)((float)memory.getHeapMemoryUsage().getUsed()/
- (float)memory.getHeapMemoryUsage().getMax());
- logger4j.debug("Heap memory usage (used/max): "+heapFraction);
--
-+
- if(readsInView.size() > checkMemAfter*2 && !waitingFrame.isVisible())
- waitingFrame.showWaiting("loading...", mainPanel);
-
-- if(heapFraction > 0.90)
-+ if(heapFraction > 0.90)
- {
- popFrame.show(
- "Using > 90 % of the maximum memory limit:"+
-@@ -835,10 +834,10 @@ public class BamView extends JPanel
- else
- return seqLengths.get((String) combo.getSelectedItem());
- }
--
-+
- /**
- * For BAM files with multiple references sequences, calculate
-- * the offset from the start of the concatenated sequence for
-+ * the offset from the start of the concatenated sequence for
- * a given reference.
- * @param refName
- * @return
-@@ -847,7 +846,7 @@ public class BamView extends JPanel
- {
- if(!isConcatSequences())
- return 0;
--
-+
- if(offsetLengths == null)
- {
- if(feature_display == null)
-@@ -867,7 +866,7 @@ public class BamView extends JPanel
- final HashMap<String, Integer> lookup = new HashMap<String, Integer>();
- for(int i=0; i<features.size(); i++)
- lookup.put(features.elementAt(i).getIDString(), features.elementAt(i).getFirstBase());
--
-+
- offsetLengths = new HashMap<String, Integer>(seqNames.size());
- for(int i=0; i<seqNames.size(); i++)
- {
-@@ -925,12 +924,12 @@ public class BamView extends JPanel
- final int seqLength = getSequenceLength();
- int start;
- int end;
--
-+
- if(startBase > 0)
- start = startBase;
- else
- start = getBaseAtStartOfView();
--
-+
- if(endBase > 0)
- end = endBase;
- else
-@@ -938,7 +937,7 @@ public class BamView extends JPanel
- end = start + nbasesInView - 1;
- if(end > seqLength)
- end = seqLength;
--
-+
- if(feature_display != null && nbasesInView < feature_display.getMaxVisibleBases())
- nbasesInView = feature_display.getMaxVisibleBases();
- }
-@@ -1077,7 +1076,7 @@ public class BamView extends JPanel
-
- laststart = start;
- lastend = end;
--
-+
- // this needs to be synchronized when cloning BAM window
- synchronized(this)
- {
-@@ -1097,7 +1096,7 @@ public class BamView extends JPanel
- drawLineView(g2, seqLength, pixPerBase, start, end);
- }
- }
--
-+
- if(isCoverage)
- coveragePanel.repaint();
- if(isSNPplot)
-@@ -1109,7 +1108,7 @@ public class BamView extends JPanel
- {
- popFrame.show(
- "Note :: Changed to the stack view to save memory.\n"+
-- "Currently this is using "+
-+ "Currently this is using "+
- (memory.getHeapMemoryUsage().getUsed()/1000000.f)+" Mb "+
- "and the maximum\nmemory limit is "+
- (memory.getHeapMemoryUsage().getMax()/1000000.f)+" Mb.",
-@@ -1138,7 +1137,7 @@ public class BamView extends JPanel
- else
- return seqLength+nbasesInView;
- }
--
-+
- /**
- * Draw the zoomed-in base view.
- * @param g2
-@@ -1147,10 +1146,10 @@ public class BamView extends JPanel
- * @param start
- * @param end
- */
-- private void drawBaseAlignment(Graphics2D g2,
-- int seqLength,
-- float pixPerBase,
-- final int start,
-+ private void drawBaseAlignment(Graphics2D g2,
-+ int seqLength,
-+ float pixPerBase,
-+ final int start,
- int end)
- {
- ruler.start = start;
-@@ -1159,7 +1158,7 @@ public class BamView extends JPanel
- int ypos = 0;
- String refSeq = null;
- int refSeqStart = start;
--
-+
- end = start + ( mainPanel.getWidth() * ALIGNMENT_PIX_PER_BASE );
- if(bases != null)
- {
-@@ -1171,9 +1170,9 @@ public class BamView extends JPanel
-
- if(refSeqStart < 1)
- refSeqStart = 1;
-- refSeq =
-+ refSeq =
- bases.getSubSequence(new Range(refSeqStart, seqEnd), Bases.FORWARD).toUpperCase();
--
-+
- ruler.refSeq = refSeq;
- }
- catch (OutOfRangeException e)
-@@ -1185,14 +1184,14 @@ public class BamView extends JPanel
- drawSelectionRange(g2, ALIGNMENT_PIX_PER_BASE, start, end, Color.PINK);
-
- g2.setStroke(new BasicStroke (2.f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND));
--
-+
- boolean drawn[] = new boolean[readsInView.size()];
- for(int i=0; i<readsInView.size(); i++)
- drawn[i] = false;
--
-+
- Rectangle r = jspView.getViewport().getViewRect();
- int nreads = readsInView.size();
--
-+
- for (int i = 0; i < nreads; i++)
- {
- try
-@@ -1238,7 +1237,7 @@ public class BamView extends JPanel
- ae.printStackTrace();
- }
- }
--
-+
- if(ypos > getHeight())
- {
- Dimension d = getPreferredSize();
-@@ -1248,7 +1247,7 @@ public class BamView extends JPanel
- }
- }
-
--
-+
- /**
- * Draw the query sequence
- * @param g2
-@@ -1256,16 +1255,16 @@ public class BamView extends JPanel
- * @param pixPerBase
- * @param ypos
- */
-- private void drawSequence(final Graphics2D g2, final BamViewRecord bamViewRecord,
-+ private void drawSequence(final Graphics2D g2, final BamViewRecord bamViewRecord,
- int ypos, String refSeq, int refSeqStart)
- {
- SAMRecord samRecord = bamViewRecord.sam;
- if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
-- samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
-+ samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
- g2.setColor(Color.black);
- else
- g2.setColor(Color.blue);
--
-+
- final Color col = g2.getColor();
- int xpos;
- int len = 0;
-@@ -1372,7 +1371,7 @@ public class BamView extends JPanel
- refPos = block.getReferenceStart() + offset - refSeqStart;
- int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
- int width = block.getLength()*ALIGNMENT_PIX_PER_BASE;
-- int nextStart =
-+ int nextStart =
- (blocks.get(i+1).getReferenceStart() + offset - refSeqStart)*ALIGNMENT_PIX_PER_BASE;
- g2.drawLine(xstart+width, ypos-(BASE_HEIGHT/2), nextStart, ypos-(BASE_HEIGHT/2));
- }
-@@ -1382,7 +1381,7 @@ public class BamView extends JPanel
- {
- refPos = blocks.get(0).getReferenceStart()+offset-refSeqStart;
- int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
--
-+
- refPos = blocks.get(blocks.size()-1).getReferenceStart()+
- blocks.get(blocks.size()-1).getLength()+offset-refSeqStart;
- int xend = (refPos+len)*ALIGNMENT_PIX_PER_BASE;
-@@ -1398,7 +1397,7 @@ public class BamView extends JPanel
- }
- }
- }
--
-+
- /**
- * Colour bases on their mapping quality.
- * @param g2
-@@ -1415,7 +1414,7 @@ public class BamView extends JPanel
- else
- g2.setColor(Color.black);
- }
--
-+
- /**
- * Draw inferred size view.
- * @param g2
-@@ -1461,7 +1460,7 @@ public class BamView extends JPanel
- int ypos = getYPos(scaleHeight, samRecord.getReadString().length()); // (getHeight() - scaleHeight) - samRecord.getReadString().length();
- if(ypos > r.getMaxY() || ypos < r.getMinY())
- continue;
--
-+
- g2.setColor(Color.black);
- drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps, ydiff);
- }
-@@ -1471,35 +1470,35 @@ public class BamView extends JPanel
- int ypos = getYPos(scaleHeight, Math.abs(samRecord.getInferredInsertSize()));
- if( (ypos > r.getMaxY() || ypos < r.getMinY()) && ypos > 0 )
- continue;
--
-+
- if(i < readsInView.size()-1)
- {
- bamViewNextRecord = readsInView.get(++i);
- samNextRecord = bamViewNextRecord.sam;
-
- if(samRecord.getReadName().equals(samNextRecord.getReadName()))
-- {
-+ {
- // draw connection between paired reads
-- if(samRecord.getAlignmentEnd() < samNextRecord.getAlignmentStart() &&
-+ if(samRecord.getAlignmentEnd() < samNextRecord.getAlignmentStart() &&
- (samNextRecord.getAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
- {
- g2.setColor(Color.LIGHT_GRAY);
-
- int offset1 = getSequenceOffset(samRecord.getReferenceName());
- int end1 = samRecord.getAlignmentEnd()+offset1-baseAtStartOfView;
--
-+
- int offset2 = getSequenceOffset(samNextRecord.getReferenceName());
- int start2 = samNextRecord.getAlignmentStart()+offset2-baseAtStartOfView;
--
-- drawTranslucentLine(g2,
-+
-+ drawTranslucentLine(g2,
- (int)(end1*pixPerBase), (int)(start2*pixPerBase), ypos);
- }
--
-+
- if(colourByCoverageColour.isSelected())
- g2.setColor(getColourByCoverageColour(bamViewRecord));
- else if( (samRecord.getReadNegativeStrandFlag() && // strand of the query (1 for reverse)
- samNextRecord.getReadNegativeStrandFlag()) ||
-- (!samRecord.getReadNegativeStrandFlag() &&
-+ (!samRecord.getReadNegativeStrandFlag() &&
- !samNextRecord.getReadNegativeStrandFlag()))
- g2.setColor(Color.red);
- else
-@@ -1519,10 +1518,10 @@ public class BamView extends JPanel
- drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight, snps, ydiff);
- }
- }
--
-+
- drawYScale(g2, scaleHeight);
- }
--
-+
- private int getYPos(int scaleHeight, int size)
- {
- if(!logScale)
-@@ -1533,25 +1532,25 @@ public class BamView extends JPanel
- return (getHeight() - scaleHeight) - logInfSize;
- }
- }
--
-+
- /**
-- * Draw the reads as lines in vertical stacks. The reads are colour
-+ * Draw the reads as lines in vertical stacks. The reads are colour
- * coded as follows:
-- *
-+ *
- * blue - reads are unique and are paired with a mapped mate
- * black - reads are unique and are not paired or have an unmapped mate
- * green - reads are duplicates
-- *
-+ *
- * @param g2
- * @param seqLength
- * @param pixPerBase
- * @param start
- * @param end
- */
-- private void drawStackView(Graphics2D g2,
-- final int seqLength,
-- final float pixPerBase,
-- final int start,
-+ private void drawStackView(Graphics2D g2,
-+ final int seqLength,
-+ final float pixPerBase,
-+ final int start,
- final int end)
- {
- drawSelectionRange(g2, pixPerBase,start, end, Color.PINK);
-@@ -1560,16 +1559,16 @@ public class BamView extends JPanel
-
- final BasicStroke stroke = new BasicStroke(
- readLnHgt,
-- BasicStroke.CAP_BUTT,
-+ BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_MITER);
- g2.setStroke(stroke);
--
-+
- final int scaleHeight;
- if(isShowScale())
- scaleHeight = 15;
- else
- scaleHeight = 0;
--
-+
- int ypos = (getHeight() - scaleHeight);
- int ydiff = (int) Math.round(1.5*readLnHgt);
-
-@@ -1579,7 +1578,7 @@ public class BamView extends JPanel
- final int baseAtStartOfView = getBaseAtStartOfView();
- g2.setColor(Color.blue);
- final Rectangle r = jspView.getViewport().getViewRect();
--
-+
- for(BamViewRecord bamViewRecord: readsInView)
- {
- SAMRecord samRecord = bamViewRecord.sam;
-@@ -1662,18 +1661,18 @@ public class BamView extends JPanel
- int ydiff = (int) Math.round(1.5*readLnHgt);
- if(isOrientation)
- ydiff= 2*ydiff;
--
-+
- g2.setStroke(stroke);
-- // positive strand
-+ // positive strand
- drawStrand(g2, false, scaleHeight, ymid-(scaleHeight/2), -ydiff, pixPerBase);
--
-+
- // negative strand
- drawStrand(g2, true, scaleHeight, ymid+(scaleHeight/2), ydiff, pixPerBase);
- }
--
--
-- private void drawStrand(Graphics2D g2,
-- boolean isStrandNegative,
-+
-+
-+ private void drawStrand(Graphics2D g2,
-+ boolean isStrandNegative,
- int scaleHeight,
- int ymid,
- int ystep,
-@@ -1685,7 +1684,7 @@ public class BamView extends JPanel
- int baseAtStartOfView = getBaseAtStartOfView();
- g2.setColor(Color.blue);
- Rectangle r = jspView.getViewport().getViewRect();
--
-+
- for(BamViewRecord bamViewRecord: readsInView)
- {
- SAMRecord samRecord = bamViewRecord.sam;
-@@ -1763,16 +1762,16 @@ public class BamView extends JPanel
- samRecord.getMateUnmappedFlag() ) // mate is unmapped
- continue;
-
-- BamViewRecord bamViewNextRecord = null;
-+ BamViewRecord bamViewNextRecord = null;
- if(i < readsInView.size()-1)
- {
- bamViewNextRecord = readsInView.get(++i);
- SAMRecord samNextRecord = bamViewNextRecord.sam;
--
-+
- final PairedRead pr = new PairedRead();
-- if(samRecord.getReadName().equals(samNextRecord.getReadName()) &&
-+ if(samRecord.getReadName().equals(samNextRecord.getReadName()) &&
- isFromSameBamFile(bamViewRecord, bamViewNextRecord, bamList))
-- {
-+ {
- if(samRecord.getAlignmentStart() < samNextRecord.getAlignmentStart())
- {
- pr.sam1 = bamViewRecord;
-@@ -1790,22 +1789,22 @@ public class BamView extends JPanel
- pr.sam1 = bamViewRecord;
- pr.sam2 = null;
- }
--
-+
- pairedReads.add(pr);
- }
- }
- Collections.sort(pairedReads, new PairedReadComparator());
--
-- Stroke originalStroke = new BasicStroke (readLnHgt, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
-+
-+ Stroke originalStroke = new BasicStroke (readLnHgt, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
-
- g2.setStroke( new BasicStroke (1.3f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND));
--
-+
- final int scaleHeight;
- if(isShowScale())
- scaleHeight = 15;
- else
- scaleHeight = 0;
--
-+
- int ydiff = (int) Math.round(2.3*readLnHgt);
- if(isOrientation)
- ydiff= 2*ydiff;
-@@ -1866,11 +1865,11 @@ public class BamView extends JPanel
- }
-
- int offset = getSequenceOffset(pr.sam1.sam.getReferenceName());
-- drawTranslucentJointedLine(g2,
-+ drawTranslucentJointedLine(g2,
- (int)( (prStart+offset-getBaseAtStartOfView())*pixPerBase),
- (int)( (prEnd +offset-getBaseAtStartOfView())*pixPerBase), ypos);
- }
--
-+
- if(colourByCoverageColour.isSelected())
- g2.setColor(getColourByCoverageColour(pr.sam1));
- else if(colourByStrandTag.isSelected())
-@@ -1879,12 +1878,12 @@ public class BamView extends JPanel
- g2.setColor(Color.BLUE);
- else if( ((Character)pr.sam1.sam.getAttribute("XS")).equals('-') )
- g2.setColor(Color.RED);
-- else
-- g2.setColor(Color.BLACK);
-+ else
-+ g2.setColor(Color.BLACK);
- }
- else if(colourByReadGrp.isSelected())
- g2.setColor(getReadGroupFrame().getReadGroupColour(readGroups, pr.sam1.sam.getReadGroup()));
-- else if( pr.sam2 != null &&
-+ else if( pr.sam2 != null &&
- !( pr.sam1.sam.getReadNegativeStrandFlag() ^ pr.sam2.sam.getReadNegativeStrandFlag() ) )
- g2.setColor(Color.red);
- else
-@@ -1899,7 +1898,7 @@ public class BamView extends JPanel
- }
- }
- }
--
-+
- /**
- * Check if a record is on the negative strand. If the RNA strand specific
- * checkbox is set then use the RNA strand.
-@@ -1907,8 +1906,8 @@ public class BamView extends JPanel
- * @param useStrandTag - strand specific tag
- * @return
- */
-- protected static boolean isNegativeStrand(final SAMRecord samRecord,
-- final boolean useStrandTag)
-+ protected static boolean isNegativeStrand(final SAMRecord samRecord,
-+ final boolean useStrandTag)
- {
- if(useStrandTag)
- {
-@@ -1921,7 +1920,7 @@ public class BamView extends JPanel
- }
- return samRecord.getReadNegativeStrandFlag();
- }
--
-+
- /**
- * Check if two records are from the same BAM file
- * @param sam1
-@@ -1929,8 +1928,8 @@ public class BamView extends JPanel
- * @param bamList
- * @return
- */
-- private boolean isFromSameBamFile(final BamViewRecord sam1,
-- final BamViewRecord sam2,
-+ private boolean isFromSameBamFile(final BamViewRecord sam1,
-+ final BamViewRecord sam2,
- final List<String> bamList)
- {
- if(bamList == null || bamList.size()<2)
-@@ -1941,18 +1940,18 @@ public class BamView extends JPanel
- if(o1 != -1 && o2 != -1)
- if( o1 != o2 )
- return false;
--
-+
- return true;
- }
--
--
-+
-+
- /**
- * Check if two records overlap
- * @param s1
- * @param s2
- * @return true id the two reads overlap
- */
-- private boolean readsOverlap(final SAMRecord s1,
-+ private boolean readsOverlap(final SAMRecord s1,
- final SAMRecord s2)
- {
- if( (s2.getAlignmentStart() >= s1.getAlignmentStart() &&
-@@ -1960,7 +1959,7 @@ public class BamView extends JPanel
- (s2.getAlignmentEnd() >= s1.getAlignmentStart() &&
- s2.getAlignmentEnd() <= s1.getAlignmentEnd()) )
- return true;
--
-+
- if( (s1.getAlignmentStart() >= s2.getAlignmentStart() &&
- s1.getAlignmentStart() <= s2.getAlignmentEnd()) ||
- (s1.getAlignmentEnd() >= s2.getAlignmentStart() &&
-@@ -1968,7 +1967,7 @@ public class BamView extends JPanel
- return true;
- return false;
- }
--
-+
- /**
- * Draw the read coverage.
- * @param g2
-@@ -2003,9 +2002,9 @@ public class BamView extends JPanel
- coverageView.drawSelectionRange(g2, pixPerBase, start, end, getHeight(), Color.PINK);
- coverageView.draw(g2, getWidth(), hgt, hideBamList);
- if(!coverageView.isPlotHeatMap())
-- coverageView.drawMax(g2, coverageView.getMaxCoverage());
-+ coverageView.drawMax(g2, coverageView.getMaxCoverage());
- }
--
-+
- /**
- * Draw a read that apparently has a read mate that is not in view.
- * @param g2
-@@ -2015,7 +2014,7 @@ public class BamView extends JPanel
- * @param originalStroke
- * @param stroke
- */
-- private void drawLoneRead(Graphics2D g2, BamViewRecord bamViewRecord, int ypos,
-+ private void drawLoneRead(Graphics2D g2, BamViewRecord bamViewRecord, int ypos,
- float pixPerBase, int baseAtStartOfView, int scaleHeight, List<Integer> snps, int ydiff)
- {
- SAMRecord samRecord = bamViewRecord.sam;
-@@ -2023,64 +2022,64 @@ public class BamView extends JPanel
- int offset = getSequenceOffset(samRecord.getReferenceName());
- int thisStart = samRecord.getAlignmentStart()+offset;
- int thisEnd = thisStart + samRecord.getReadString().length() -1;
--
-+
- if(ypos <= 0)
- {
- offTheTop = true;
- ypos = samRecord.getReadString().length();
- }
--
-+
- if(samRecord.getInferredInsertSize() == 0)
- {
- offTheTop = true;
- ypos = getHeight() - scaleHeight - 5;
- }
--
-+
- if(samRecord.getInferredInsertSize() != 0 &&
- Math.abs(samRecord.getMateAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
- {
- g2.setColor(Color.LIGHT_GRAY);
--
-+
- if(samRecord.getAlignmentEnd() < samRecord.getMateAlignmentStart())
- {
-- int nextStart =
-+ int nextStart =
- (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
-- drawTranslucentLine(g2,
-+ drawTranslucentLine(g2,
- (int)((thisEnd-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
- }
- else
- {
-- int nextStart =
-+ int nextStart =
- (int)((samRecord.getMateAlignmentStart()-getBaseAtStartOfView()+offset)*pixPerBase);
-- drawTranslucentLine(g2,
-+ drawTranslucentLine(g2,
- (int)((thisStart-getBaseAtStartOfView())*pixPerBase), nextStart, ypos);
- }
- }
--
-+
- if(colourByCoverageColour.isSelected())
- g2.setColor(getColourByCoverageColour(bamViewRecord));
- else if(offTheTop)
-- g2.setColor(DARK_ORANGE);
-+ g2.setColor(DARK_ORANGE);
- else if(samRecord.getReadNegativeStrandFlag() &&
- samRecord.getMateNegativeStrandFlag()) // strand of the query (1 for reverse)
- g2.setColor(Color.red);
- else
- g2.setColor(Color.blue);
--
-+
- drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps, ydiff);
--
-+
- /*if (isSNPs)
- showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);*/
- }
-
--
-+
- private void drawScale(Graphics2D g2, int start, int end, float pixPerBase, int ypos)
- {
- g2.setColor(Color.black);
- g2.drawLine( 0, ypos-14,
- (int)((end - getBaseAtStartOfView())*pixPerBase), ypos-14);
- int interval = end-start;
--
-+
- if(interval > 256000)
- drawTicks(g2, start, end, pixPerBase, 512000, ypos);
- else if(interval > 64000)
-@@ -2094,14 +2093,14 @@ public class BamView extends JPanel
- else
- drawTicks(g2, start, end, pixPerBase, 100, ypos);
- }
--
-+
- private void drawTicks(Graphics2D g2, int start, int end, float pixPerBase, int division, int ypos)
- {
- int markStart = (Math.round(start/division)*division);
--
-+
- if(markStart < 1)
- markStart = 1;
--
-+
- int sm = markStart-(division/2);
- float x;
- if(sm > start)
-@@ -2109,26 +2108,26 @@ public class BamView extends JPanel
- x = (sm-getBaseAtStartOfView())*pixPerBase;
- g2.drawLine((int)x, ypos-14,(int)x, ypos-12);
- }
--
-+
- for(int m=markStart; m<end; m+=division)
- {
- x = (m-getBaseAtStartOfView())*pixPerBase;
- g2.drawString(Integer.toString(m), x, ypos-1);
- g2.drawLine((int)x, ypos-14,(int)x, ypos-11);
--
-+
- sm = m+(division/2);
--
-+
- if(sm < end)
- {
- x = (sm-getBaseAtStartOfView())*pixPerBase;
- g2.drawLine((int)x, ypos-14,(int)x, ypos-12);
- }
--
-+
- if(m == 1)
- m = 0;
- }
- }
--
-+
- /**
- * Draw a y-scale for inferred size (isize) of reads.
- * @param g2
-@@ -2138,13 +2137,13 @@ public class BamView extends JPanel
- {
- g2.setColor(Color.black);
- int maxY = getPreferredSize().height-xScaleHeight;
--
-+
- if(logScale)
- {
- int start = 10;
- int count = 0;
- int ypos = getYPos(xScaleHeight, start);
--
-+
- while(ypos > 0 && count < 15 && start > 1)
- {
- g2.drawLine(0, ypos, 2, ypos);
-@@ -2155,7 +2154,7 @@ public class BamView extends JPanel
- }
- return;
- }
--
-+
- for(int i=100; i<maxY; i+=100)
- {
- int ypos = getHeight()-i-xScaleHeight;
-@@ -2163,7 +2162,7 @@ public class BamView extends JPanel
- g2.drawString(Integer.toString(i), 3, ypos);
- }
- }
--
-+
- /**
- * Draw a given read.
- * @param g2
-@@ -2173,7 +2172,7 @@ public class BamView extends JPanel
- * @param baseAtStartOfView
- * @param snps
- */
-- private void drawRead(Graphics2D g2,
-+ private void drawRead(Graphics2D g2,
- final BamViewRecord bamViewRecord,
- final float pixPerBase,
- final int ypos,
-@@ -2240,7 +2239,7 @@ public class BamView extends JPanel
- lastEnd = blockEnd;
- }
- }
--
-+
- if(isOrientation)
- drawArrow(g2, thisRead, thisStart, thisEnd, pixPerBase, ypos, ydiff);
-@@ -2271,16 +2270,16 @@ public class BamView extends JPanel
- * @param ypos
- */
- private void drawArrow(final Graphics2D g2,
-- final SAMRecord thisRead,
-- final int thisStart,
-- final int thisEnd,
-- final float pixPerBase,
-+ final SAMRecord thisRead,
-+ final int thisStart,
-+ final int thisEnd,
-+ final float pixPerBase,
- int ypos,
- int ydiff)
- {
- if(ydiff < 0)
- ydiff = -ydiff;
--
-+
- if(thisRead.getReadNegativeStrandFlag())
- {
- ypos-=readLnHgt/2;
-@@ -2294,9 +2293,9 @@ public class BamView extends JPanel
- int apos = ypos - ydiff + 1;
- g2.drawLine((int)( (thisEnd-5) * pixPerBase), apos,
- (int)( thisEnd * pixPerBase), ypos);
-- }
-+ }
- }
--
-+
- /**
- * Highlight a selected range
- * @param g2
-@@ -2314,19 +2313,19 @@ public class BamView extends JPanel
- {
- int rangeStart = selectedRange.getStart();
- int rangeEnd = selectedRange.getEnd();
--
-+
- if(end < rangeStart || start > rangeEnd)
- return;
--
-+
- int x = (int) (pixPerBase*(rangeStart-getBaseAtStartOfView()));
- int width = (int) (pixPerBase*(rangeEnd-rangeStart+1));
--
-+
- g2.setColor(c);
- g2.fillRect(x, 0, width, getHeight());
- }
- }
- }
--
-+
- /**
- * Draw a translucent line
- * @param g2
-@@ -2341,7 +2340,7 @@ public class BamView extends JPanel
- g2.drawLine(start, ypos, end, ypos);
- g2.setComposite(origComposite);
- }
--
-+
- /**
- * Draw a translucent line
- * @param g2
-@@ -2353,14 +2352,14 @@ public class BamView extends JPanel
- {
- Composite origComposite = g2.getComposite();
- g2.setComposite(translucent);
--
-+
- int mid = (int) ((end-start)/2.f)+start;
- //g2.drawLine(start, ypos, end, ypos);
- g2.drawLine(start, ypos, mid, ypos-5);
- g2.drawLine(mid, ypos-5, end, ypos);
- g2.setComposite(origComposite);
- }
--
-+
- /**
- * Display the SNPs for the given read.
- * @param snps
-@@ -2375,18 +2374,18 @@ public class BamView extends JPanel
- final Stroke originalStroke = g2.getStroke();
- final BasicStroke stroke = new BasicStroke(
- 1.3f,
-- BasicStroke.CAP_BUTT,
-+ BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_MITER);
- g2.setStroke(stroke);
--
-+
- g2.setColor(Color.red);
- for(int pos: snps)
- g2.drawLine((int) (pos * pixPerBase), ypos + 2,
- (int) (pos * pixPerBase), ypos - 2);
- g2.setStroke(originalStroke);
- }
--
--
-+
-+
- /**
- * Get the SNP positions
- * @param samRecord
-@@ -2399,7 +2398,7 @@ public class BamView extends JPanel
- int rend = samRecord.getAlignmentEnd();
- int offset = getSequenceOffset(samRecord.getReferenceName());
- ArrayList<Integer> snps = null;
--
-+
- // use alignment blocks of the contiguous alignment of
- // subsets of read bases to a reference sequence
- try
-@@ -2440,8 +2439,8 @@ public class BamView extends JPanel
- }
- return snps;
- }
--
--
-+
-+
- /**
- * Add the alignment view to the supplied <code>JPanel</code> in
- * a <code>JScrollPane</code>.
-@@ -2454,7 +2453,7 @@ public class BamView extends JPanel
- {
- final JComponent topPanel = bamTopPanel(frame);
- mainPanel.setPreferredSize(new Dimension(900, 400));
--
-+
- setDisplay(1, nbasesInView, null);
- mainPanel.setLayout(new BorderLayout());
-
-@@ -2469,7 +2468,7 @@ public class BamView extends JPanel
- //
- snpPanel = new SnpPanel(this, bases);
- bottomPanel.add(snpPanel, BorderLayout.NORTH);
--
-+
- if(feature_display == null)
- {
- scrollBar = new JScrollBar(JScrollBar.HORIZONTAL, 1, nbasesInView, 1,
-@@ -2514,7 +2513,7 @@ public class BamView extends JPanel
- "The length of the sequence loaded does not match the length of",
- "the default reference sequence in the BAM/CRAM ("+seqNames.get(0)+").",
- (newIndex == -1 ? "" : "The length does match the reference "+
-- seqNames.get(newIndex)+" so this has been set as the default.")
-+ seqNames.get(newIndex)+" so this has been set as the default.")
- };
- new NonModalDialog(frame, label);
- }
-@@ -2532,13 +2531,13 @@ public class BamView extends JPanel
- jspView.getVerticalScrollBar().setValue(
- jspView.getVerticalScrollBar().getMaximum());
- }
--
-+
- private void addToViewMenu(final short thisBamIndex)
- {
- final File f = new File(bamList.get(thisBamIndex));
- final JCheckBoxMenuItem cbBam = new JCheckBoxMenuItem(
-- f.getName(),
-- getImageIcon(getColourByCoverageColour(thisBamIndex)),
-+ f.getName(),
-+ getImageIcon(getColourByCoverageColour(thisBamIndex)),
- true);
- bamFilesMenu.add(cbBam);
- cbBam.addItemListener(new ItemListener() {
-@@ -2549,10 +2548,10 @@ public class BamView extends JPanel
- hideBamList.add(new Short(thisBamIndex));
- laststart = -1;
- repaint();
-- }
-+ }
- });
- }
--
-+
- /**
- * Refresh the colour of the icons used to identify the
- * BAM/CRAM files.
-@@ -2571,7 +2570,7 @@ public class BamView extends JPanel
- }
- }
- }
--
-+
- protected Color getColorByJCheckBoxMenuItem(JCheckBoxMenuItem cbBam)
- {
- final String bam = cbBam.getText();
-@@ -2583,7 +2582,7 @@ public class BamView extends JPanel
- }
- return null;
- }
--
-+
- /**
- * Create an icon of a box using the given colour.
- * @param c
-@@ -2610,16 +2609,16 @@ public class BamView extends JPanel
- null, false, "BamView", "BAM/CRAM");
- List<String> bamFiles = bamFileSelection.getFiles(BAM_SUFFIX);
- short count = (short) bamList.size();
--
-+
- bamList.addAll(bamFileSelection.getFiles(BAM_SUFFIX));
--
-+
- for(short i=0; i<bamFiles.size(); i++)
- addToViewMenu((short) (i+count));
-- laststart = -1;
-+ laststart = -1;
- repaint();
-- }
-+ }
- });
--
-+
- bamFilesMenu.setFont(addBam.getFont());
-
- final JMenuItem groupBams = new JMenuItem("Group BAMs/CRAMs ...");
-@@ -2633,7 +2632,7 @@ public class BamView extends JPanel
- bamFilesMenu.addSeparator();
- menu.add(bamFilesMenu);
-
--
-+
- final JMenu analyse = new JMenu("Analyse");
- menu.add(analyse);
- final JMenuItem readCount = new JMenuItem("Read count of selected features ...");
-@@ -2652,18 +2651,18 @@ public class BamView extends JPanel
- Box yBox = Box.createVerticalBox();
- yBox.add(overlap);
- yBox.add(spliced);
--
-+
- final ReadCountDialog opts = new ReadCountDialog(new JFrame(),
- "Read Count Options", feature_display, yBox);
- if(opts.getStatus() == -1)
- return;
- //JOptionPane.showMessageDialog(null, yBox, "Read Count Option", JOptionPane.INFORMATION_MESSAGE);
--
-+
- new MappedReads(BamView.this, features,
- !overlap.isSelected(), spliced.isSelected(), colourByStrandTag.isSelected());
-- }
-+ }
- });
--
-+
- final JMenuItem rpkm = new JMenuItem("RPKM value of selected features ...");
- analyse.add(rpkm);
- if(feature_display == null)
-@@ -2678,14 +2677,14 @@ public class BamView extends JPanel
- overlap.setToolTipText("Include reads that partially overlap the feature");
- JCheckBox spliced = new JCheckBox("Introns included", true);
- JCheckBox allRefSeqs = new JCheckBox("Use reads mapped to all reference sequences", false);
--
-+
- Box yBox = Box.createVerticalBox();
- yBox.add(overlap);
- yBox.add(spliced);
--
-+
- if(seqLengths.size() > 1)
- yBox.add(allRefSeqs);
--
-+
- final ReadCountDialog opts = new ReadCountDialog(new JFrame(),
- "RPKM Options", feature_display, yBox);
- if(opts.getStatus() == -1)
-@@ -2696,7 +2695,7 @@ public class BamView extends JPanel
- seqlen = feature_display.getSequenceLength();
- else if(bases != null)
- seqlen = bases.getLength();
--
-+
- new MappedReads(BamView.this, features, seqlen,
- !overlap.isSelected(), spliced.isSelected(), allRefSeqs.isSelected(),
- colourByStrandTag.isSelected());
-@@ -2714,14 +2713,14 @@ public class BamView extends JPanel
- if(feature_display == null)
- return;
- new CreateFeatures(groupsFrame);
-- }
-+ }
- });
-
- for(short i=0; i<bamList.size(); i++)
- addToViewMenu(i);
--
-+
- menu.add(new JSeparator());
--
-+
- JMenu viewMenu = new JMenu("Views");
- cbStackView.setFont(viewMenu.getFont());
- cbIsizeStackView.setFont(viewMenu.getFont());
-@@ -2730,13 +2729,13 @@ public class BamView extends JPanel
- cbCoverageView.setFont(viewMenu.getFont());
- cbCoverageStrandView.setFont(viewMenu.getFont());
- cbCoverageHeatMap.setFont(viewMenu.getFont());
--
-+
- baseQualityColour.setFont(viewMenu.getFont());
- colourByReadGrp.setFont(viewMenu.getFont());
- colourByCoverageColour.setFont(viewMenu.getFont());
- colourByStrandTag.setFont(viewMenu.getFont());
- markInsertions.setFont(viewMenu.getFont());
--
-+
- cbIsizeStackView.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
-@@ -2748,8 +2747,8 @@ public class BamView extends JPanel
- }
- });
- viewMenu.add(cbIsizeStackView);
--
--
-+
-+
- cbStackView.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
-@@ -2763,7 +2762,7 @@ public class BamView extends JPanel
- }
- });
- viewMenu.add(cbStackView);
--
-+
-
- cbPairedStackView.addActionListener(new ActionListener()
- {
-@@ -2777,7 +2776,7 @@ public class BamView extends JPanel
- }
- });
- viewMenu.add(cbPairedStackView);
--
-+
- cbStrandStackView.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
-@@ -2793,7 +2792,7 @@ public class BamView extends JPanel
- }
- });
- viewMenu.add(cbStrandStackView);
--
-+
- cbCoverageView.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
-@@ -2811,7 +2810,7 @@ public class BamView extends JPanel
- }
- });
- viewMenu.add(cbCoverageView);
--
-+
- cbCoverageStrandView.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
-@@ -2830,8 +2829,8 @@ public class BamView extends JPanel
- }
- });
- viewMenu.add(cbCoverageStrandView);
--
--
-+
-+
- cbCoverageHeatMap.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
-@@ -2849,20 +2848,20 @@ public class BamView extends JPanel
- }
- });
- viewMenu.add(cbCoverageHeatMap);
--
-+
- menu.add(viewMenu);
--
-+
- final JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNP marks", isSNPs);
-- //
-+ //
- final JMenu colourMenu = new JMenu("Colour By");
--
-+
- final JCheckBoxMenuItem colourDefault = new JCheckBoxMenuItem ("Default", true);
- final ButtonGroup grp = new ButtonGroup();
- grp.add(colourByReadGrp);
- grp.add(colourByCoverageColour);
- grp.add(colourByStrandTag);
- grp.add(colourDefault);
--
-+
- colourMenu.add(colourDefault);
- colourDefault.addActionListener(new ActionListener()
- {
-@@ -2871,7 +2870,7 @@ public class BamView extends JPanel
- repaintBamView();
- }
- });
--
-+
- colourMenu.add(colourByReadGrp);
- colourByReadGrp.addActionListener(new ActionListener()
- {
-@@ -2880,7 +2879,7 @@ public class BamView extends JPanel
- repaintBamView();
- }
- });
--
-+
- colourMenu.add(colourByCoverageColour);
- colourByCoverageColour.addActionListener(new ActionListener()
- {
-@@ -2889,7 +2888,7 @@ public class BamView extends JPanel
- repaintBamView();
- }
- });
--
-+
- colourMenu.add(colourByStrandTag);
- colourByStrandTag.addActionListener(new ActionListener()
- {
-@@ -2932,7 +2931,7 @@ public class BamView extends JPanel
- }
- });
- showMenu.add(checkBoxOrientation);
--
-+
- JCheckBoxMenuItem checkBoxSingle = new JCheckBoxMenuItem("Single Reads");
- checkBoxSingle.addActionListener(new ActionListener()
- {
-@@ -2943,7 +2942,7 @@ public class BamView extends JPanel
- }
- });
- showMenu.add(checkBoxSingle);
--
-+
- checkBoxSNPs.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
-@@ -2955,14 +2954,14 @@ public class BamView extends JPanel
- JOptionPane.INFORMATION_MESSAGE);
- }
- isSNPs = !isSNPs;
--
-+
- if(isSNPs)
- baseQualityColour.setSelected(false);
- repaint();
- }
- });
- showMenu.add(checkBoxSNPs);
--
-+
- markInsertions.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
-@@ -2972,7 +2971,7 @@ public class BamView extends JPanel
- });
- showMenu.add(markInsertions);
- menu.add(showMenu);
--
-+
- //
- JMenu graphMenu = new JMenu("Graph");
- JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage", isCoverage);
-@@ -2982,9 +2981,9 @@ public class BamView extends JPanel
- {
- isCoverage = !isCoverage;
- coveragePanel.setVisible(isCoverage);
--
-- if( isCoverage &&
-- !cbCoverageView.isSelected() &&
-+
-+ if( isCoverage &&
-+ !cbCoverageView.isSelected() &&
- !cbCoverageStrandView.isSelected() &&
- !cbCoverageHeatMap.isSelected())
- laststart = -1;
-@@ -2992,7 +2991,7 @@ public class BamView extends JPanel
- }
- });
- graphMenu.add(checkBoxCoverage);
--
-+
- JCheckBoxMenuItem checkBoxSNP = new JCheckBoxMenuItem("SNP", isSNPplot);
- checkBoxSNP.addActionListener(new ActionListener()
- {
-@@ -3006,8 +3005,8 @@ public class BamView extends JPanel
- });
- graphMenu.add(checkBoxSNP);
- menu.add(graphMenu);
--
--
-+
-+
- if(feature_display != null)
- {
- final JCheckBoxMenuItem checkBoxSync =
-@@ -3021,15 +3020,15 @@ public class BamView extends JPanel
- });
- menu.add(checkBoxSync);
- }
--
-+
- menu.add(new JSeparator());
-
- JMenu maxHeightMenu = new JMenu("BamView Height");
- menu.add(maxHeightMenu);
--
-+
- final String hgts[] =
- {"500", "800", "1000", "1500", "2500", "5000", "50000"};
--
-+
- ButtonGroup bgroup = new ButtonGroup();
- for(int i=0; i<hgts.length; i++)
- {
-@@ -3049,12 +3048,12 @@ public class BamView extends JPanel
- }
- });
- }
--
-+
- menu.add(new JSeparator());
- logMenuItem.setFont(menu.getFont());
- menu.add(logMenuItem);
- logMenuItem.setEnabled(isIsizeStackView());
--
-+
- logMenuItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
-@@ -3063,7 +3062,7 @@ public class BamView extends JPanel
- repaint();
- }
- });
--
-+
- final JMenuItem readGroupsMenu = new JMenuItem("Read Groups ...");
- readGroupsMenu.addActionListener(new ActionListener(){
- public void actionPerformed(ActionEvent arg0)
-@@ -3073,7 +3072,7 @@ public class BamView extends JPanel
- }
- });
- menu.add(readGroupsMenu);
--
-+
- JMenuItem filter = new JMenuItem("Filter Reads ...");
- menu.add(filter);
- filter.addActionListener(new ActionListener()
-@@ -3084,9 +3083,9 @@ public class BamView extends JPanel
- filterFrame = new SAMRecordFilter(BamView.this);
- else
- filterFrame.setVisible(true);
-- }
-+ }
- });
--
-+
- JMenuItem maxReadCoverage = new JMenuItem("Read Coverage Threshold ...");
- menu.add(maxReadCoverage);
- maxReadCoverage.addActionListener(new ActionListener()
-@@ -3095,7 +3094,7 @@ public class BamView extends JPanel
- {
- final TextFieldInt maxRead = new TextFieldInt();
- maxRead.setValue(MAX_COVERAGE);
-- int status = JOptionPane.showConfirmDialog(null, maxRead,
-+ int status = JOptionPane.showConfirmDialog(null, maxRead,
- "Read Coverage Threshold", JOptionPane.OK_CANCEL_OPTION);
- if(status == JOptionPane.OK_OPTION &&
- maxRead.getValue() != MAX_COVERAGE)
-@@ -3106,9 +3105,9 @@ public class BamView extends JPanel
- laststart = -1;
- repaint();
- }
-- }
-+ }
- });
--
-+
- JMenuItem readList = new JMenuItem("List Reads ...");
- menu.add(readList);
- readList.addActionListener(new ActionListener()
-@@ -3125,7 +3124,7 @@ public class BamView extends JPanel
- public void actionPerformed(ActionEvent e)
- {
- openBamView(new Vector<String>(bamList));
-- }
-+ }
- });
- menu.add(new JSeparator());
- menu.add(bamSplitter);
-@@ -3137,14 +3136,14 @@ public class BamView extends JPanel
- viewMenu.add(new JSeparator());
- viewMenu.add(coverageMenu);
- }
--
-+
- private ReadGroupsFrame getReadGroupFrame()
- {
- if(readGrpFrame == null)
- readGrpFrame = new ReadGroupsFrame(readGroups, BamView.this);
- return readGrpFrame;
- }
--
-+
- private JComponent bamTopPanel(final JFrame frame)
- {
- final JComponent topPanel;
-@@ -3152,13 +3151,13 @@ public class BamView extends JPanel
- {
- topPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0));
- if(feature_display != null)
-- this.selection = feature_display.getSelection();
-+ this.selection = feature_display.getSelection();
- }
- else
-- {
-+ {
- topPanel = new JMenuBar();
- frame.setJMenuBar((JMenuBar)topPanel);
--
-+
- JMenu fileMenu = new JMenu("File");
- topPanel.add(fileMenu);
-
-@@ -3170,21 +3169,21 @@ public class BamView extends JPanel
- {
- String[] s = { "NEW-BAMVIEW" };
- BamView.main(s);
-- }
-+ }
- });
--
--
-+
-+
- JMenuItem saveAs = new JMenuItem("Save As Image File (png/jpeg/svg) ...");
- fileMenu.add(saveAs);
- saveAs.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
-- PrintBamView.print((JPanel)mainPanel.getParent());
-+ PrintBamView.print((JPanel)mainPanel.getParent());
- }
- });
-
--
-+
- JMenuItem close = new JMenuItem("Close");
- fileMenu.add(close);
- close.addActionListener(new ActionListener()
-@@ -3202,15 +3201,15 @@ public class BamView extends JPanel
- {
- public void actionPerformed(ActionEvent e)
- {
-- int status = JOptionPane.showConfirmDialog(BamView.this,
-- "Exit BamView?", "Exit",
-+ int status = JOptionPane.showConfirmDialog(BamView.this,
-+ "Exit BamView?", "Exit",
- JOptionPane.OK_CANCEL_OPTION);
- if(status != JOptionPane.OK_OPTION)
- return;
- System.exit(0);
-- }
-+ }
- });
--
-+
- addKeyListener(new KeyAdapter()
- {
- public void keyPressed(final KeyEvent event)
-@@ -3231,13 +3230,13 @@ public class BamView extends JPanel
- }
- });
- }
--
-+
- if(seqNames.size() > 1)
- {
- int len = 0;
- for(int i=0; i<seqNames.size(); i++)
- len += seqLengths.get(seqNames.get(i));
--
-+
- if(feature_display != null &&
- len == feature_display.getSequenceLength())
- concatSequences = true;
-@@ -3255,7 +3254,7 @@ public class BamView extends JPanel
- {
- handleCanvasMouseDrag(event);
- }
--
-+
- public void mouseMoved(MouseEvent e)
- {
- lastMousePoint = e.getPoint();
-@@ -3362,10 +3361,10 @@ public class BamView extends JPanel
- });
- topPanel.add(zoomOut);
- }
--
-+
- topPanel.add(buttonAutoHide);
--
--
-+
-+
- final JSlider slider = new JSlider(13, 52, (int) (readLnHgt*10));
- slider.addChangeListener(new ChangeListener(){
- public void stateChanged(ChangeEvent arg0)
-@@ -3376,7 +3375,7 @@ public class BamView extends JPanel
- });
- topPanel.add(new JLabel(" Read Height:"));
- topPanel.add(slider);
--
-+
- if(feature_display != null)
- {
- JButton close = new JButton("Close");
-@@ -3397,26 +3396,26 @@ public class BamView extends JPanel
- }
- return topPanel;
- }
--
-+
- public void setVisible(boolean visible)
- {
- super.setVisible(visible);
- mainPanel.setVisible(visible);
- }
--
-+
- private void setViewportMidPoint()
- {
- Point p = jspView.getViewport().getLocation();
- p.y = (getHeight() - jspView.getViewport().getViewRect().height)/2;
- jspView.getViewport().setViewPosition(p);
- }
--
-+
- private void setViewportBtm()
- {
- jspView.getVerticalScrollBar().setValue(
- jspView.getVerticalScrollBar().getMaximum());
- }
--
-+
- protected int getBaseAtStartOfView()
- {
- if(feature_display != null)
-@@ -3424,7 +3423,7 @@ public class BamView extends JPanel
- else
- return scrollBar.getValue();
- }
--
-+
- /**
- * Set the panel size based on the number of bases visible
- * and repaint.
-@@ -3434,14 +3433,14 @@ public class BamView extends JPanel
- {
- int startValue = getBaseAtStartOfView();
- this.nbasesInView = nbasesInView;
-- float pixPerBase = getPixPerBaseByWidth();
-+ float pixPerBase = getPixPerBaseByWidth();
-
- if(isBaseAlignmentView(pixPerBase))
- {
- pixPerBase = ALIGNMENT_PIX_PER_BASE;
- this.nbasesInView = (int)(mainPanel.getWidth()/pixPerBase);
- jspView.getVerticalScrollBar().setValue(0);
--
-+
- if(ruler == null)
- ruler = new Ruler();
- jspView.setColumnHeaderView(ruler);
-@@ -3475,14 +3474,14 @@ public class BamView extends JPanel
-
- if(scrollBar != null)
- {
-- scrollBar.setValues(startValue, nbasesInView, 1,
-+ scrollBar.setValues(startValue, nbasesInView, 1,
- getMaxBasesInPanel(getSequenceLength()));
- scrollBar.setUnitIncrement(nbasesInView/20);
- scrollBar.setBlockIncrement(nbasesInView);
- }
- }
-
--
-+
- /**
- * Set the start and end base positions to display.
- * @param start
-@@ -3508,32 +3507,32 @@ public class BamView extends JPanel
- else
- pixPerBase = feature_display.getWidth()/(float)(end-start+1);
- }
--
-+
- Dimension d = new Dimension();
- d.setSize(nbasesInView*pixPerBase, maxHeight);
- setPreferredSize(d);
--
-+
- if(event == null)
- {
- this.startBase = -1;
- this.endBase = -1;
- }
- }
--
-+
- /**
-- * Return an Artemis entry from a file
-+ * Return an Artemis entry from a file
- * @param entryFileName
- * @param entryGroup
- * @return
- * @throws NoSequenceException
- */
-- private Entry getEntry(final String entryFileName, final EntryGroup entryGroup)
-+ private Entry getEntry(final String entryFileName, final EntryGroup entryGroup)
- throws NoSequenceException
- {
- final Document entry_document = DocumentFactory.makeDocument(entryFileName);
- final EntryInformation artemis_entry_information =
- Options.getArtemisEntryInformation();
--
-+
- //System.out.println(entryFileName);
- final uk.ac.sanger.artemis.io.Entry new_embl_entry =
- EntryFileDialog.getEntryFromFile(null, entry_document,
-@@ -3548,7 +3547,7 @@ public class BamView extends JPanel
- {
- if(entryGroup.getSequenceEntry() != null)
- bases = entryGroup.getSequenceEntry().getBases();
--
-+
- if(bases == null)
- {
- entry = new Entry(new_embl_entry);
-@@ -3556,10 +3555,10 @@ public class BamView extends JPanel
- }
- else
- entry = new Entry(bases,new_embl_entry);
--
-+
- entryGroup.add(entry);
-- }
-- catch(OutOfRangeException e)
-+ }
-+ catch(OutOfRangeException e)
- {
- new MessageDialog(null, "read failed: one of the features in " +
- entryFileName + " has an out of range " +
-@@ -3567,7 +3566,7 @@ public class BamView extends JPanel
- }
- return entry;
- }
--
-+
- private boolean isShowScale()
- {
- return (feature_display == null ? true : false);
-@@ -3611,17 +3610,17 @@ public class BamView extends JPanel
- int seqLength = getSequenceLength();
- float pixPerBase = getPixPerBaseByWidth();
- int start = (int) ( ( (event.getPoint().getX())/pixPerBase) + getBaseAtStartOfView() );
--
-+
- if(start < 1)
- start = 1;
- if(start > seqLength)
- start = seqLength;
--
-+
- if (dragStart < 0 && (event.getModifiersEx() & onmask) == onmask)
- dragStart = start;
- else if((event.getModifiersEx() & onmask) != onmask)
- dragStart = -1;
--
-+
- MarkerRange drag_range;
- try
- {
-@@ -3637,7 +3636,7 @@ public class BamView extends JPanel
- e.printStackTrace();
- }
- }
--
-+
- /**
- * Get the colour for the given read given to it by the coverage plot.
- * @param samRecord
-@@ -3648,60 +3647,60 @@ public class BamView extends JPanel
- short fileIndex = 0;
- if(bamList.size()>1)
- fileIndex = samRecord.bamIndex;
-- return getColourByCoverageColour(fileIndex);
-+ return getColourByCoverageColour(fileIndex);
- }
--
-+
- private Color getColourByCoverageColour(final short fileIndex)
- {
- LineAttributes lines[] = CoveragePanel.getLineAttributes(bamList.size());
-- return lines[fileIndex].getLineColour();
-+ return lines[fileIndex].getLineColour();
- }
--
-+
-
- protected int getMaxBases()
- {
- return MAX_BASES;
- }
--
-+
- protected void setMaxBases(int max)
- {
- MAX_BASES = max;
- }
--
-+
- private boolean isStackView()
- {
-- return cbStackView.isSelected();
-+ return cbStackView.isSelected();
- }
--
-+
- private boolean isPairedStackView()
- {
- return cbPairedStackView.isSelected();
- }
--
-+
- private boolean isStrandStackView()
- {
- return cbStrandStackView.isSelected();
- }
--
-+
- private boolean isCoverageView(float pixPerBase)
- {
- if(isBaseAlignmentView(pixPerBase))
- return false;
- return cbCoverageView.isSelected() || cbCoverageStrandView.isSelected() || cbCoverageHeatMap.isSelected();
- }
--
-+
- private boolean isIsizeStackView()
- {
- return cbIsizeStackView.isSelected();
- }
--
-+
- private boolean isBaseAlignmentView(float pixPerBase)
- {
- if(pixPerBase*1.08f >= ALIGNMENT_PIX_PER_BASE)
- return true;
- return false;
- }
--
-+
- private JCheckBoxMenuItem getSelectedCheckBoxMenuItem()
- {
- if(isStackView())
-@@ -3718,37 +3717,37 @@ public class BamView extends JPanel
- return cbCoverageHeatMap;
- return cbCoverageStrandView;
- }
--
-+
- protected Selection getSelection()
- {
- return selection;
- }
--
-+
- protected List<BamViewRecord> getReadsInView()
- {
- return readsInView;
- }
--
-+
- protected int getBasesInView()
- {
- return nbasesInView;
- }
--
-+
- protected void setHighlightSAMRecord(BamViewRecord highlightSAMRecord)
- {
- this.highlightSAMRecord = highlightSAMRecord;
- }
--
-+
- protected BamViewRecord getHighlightSAMRecord()
- {
- return highlightSAMRecord;
- }
--
-+
- protected FeatureDisplay getFeatureDisplay()
- {
- return feature_display;
- }
--
-+
- /**
- * @return the combo
- */
-@@ -3798,13 +3797,13 @@ public class BamView extends JPanel
- }
- return null;
- }
--
-+
- /**
- * Open another BamView window
- */
- public void openBamView(final List<String> bamsList)
- {
-- BamView bamView = new BamView(bamsList,
-+ BamView bamView = new BamView(bamsList,
- null, nbasesInView, entry_edit,
- feature_display, bases, (JPanel) mainPanel.getParent(), null);
- bamView.getJspView().getVerticalScrollBar().setValue(
-@@ -3818,10 +3817,10 @@ public class BamView extends JPanel
- {
- feature_display.addDisplayAdjustmentListener(bamView);
- feature_display.getSelection().addSelectionChangeListener(bamView);
--
-+
- if(entry_edit != null)
- entry_edit.getOneLinePerEntryDisplay().addDisplayAdjustmentListener(bamView);
-- if(feature_display.getEntryGroup().getSequenceEntry().getEMBLEntry().getSequence()
-+ if(feature_display.getEntryGroup().getSequenceEntry().getEMBLEntry().getSequence()
- instanceof uk.ac.sanger.artemis.io.IndexFastaStream)
- {
- if(entry_edit != null)
-@@ -3833,7 +3832,7 @@ public class BamView extends JPanel
- }
- }
- }
--
-+
- /**
- * Artemis event notification
- */
-@@ -3841,8 +3840,8 @@ public class BamView extends JPanel
- {
- if(event.getType() == DisplayAdjustmentEvent.REV_COMP_EVENT &&
- event.isRevCompDisplay())
-- JOptionPane.showMessageDialog(this,
-- "Flipping the display is not supported by BamView.", "Warning",
-+ JOptionPane.showMessageDialog(this,
-+ "Flipping the display is not supported by BamView.", "Warning",
- JOptionPane.WARNING_MESSAGE);
-
- if(!asynchronous)
-@@ -3851,7 +3850,7 @@ public class BamView extends JPanel
- displayAdjustmentWork(event);
- return;
- }
--
-+
- SwingWorker worker = new SwingWorker()
- {
- public Object construct()
-@@ -3864,13 +3863,13 @@ public class BamView extends JPanel
- {
- e.printStackTrace();
- }
--
-+
- if(event.getStart() != ((FeatureDisplay)event.getSource()).getForwardBaseAtLeftEdge())
- {
- waitingFrame.showWaiting("waiting...", mainPanel);
- return null;
- }
--
-+
- displayAdjustmentWork(event);
- waitingFrame.setVisible(false);
- return null;
-@@ -3878,7 +3877,7 @@ public class BamView extends JPanel
- };
- worker.start();
- }
--
-+
- /**
- * Carry out the display agjustment event action.
- * @param event
-@@ -3898,17 +3897,17 @@ public class BamView extends JPanel
- }
- else
- {
-- setDisplay(event.getStart(),
-+ setDisplay(event.getStart(),
- event.getStart()+feature_display.getMaxVisibleBases(), event);
- repaint();
- }
- }
--
-+
- public void selectionChanged(SelectionChangeEvent event)
- {
- repaint();
- }
--
-+
- private class Ruler extends JPanel
- {
- private static final long serialVersionUID = 1L;
-@@ -3941,14 +3940,14 @@ public class BamView extends JPanel
- int xpos = (i-start)*ALIGNMENT_PIX_PER_BASE;
- g2.drawString(Integer.toString(i), xpos, ypos);
- }
--
-+
- for(int i=startMark; i<end; i+=10)
- {
- int xpos = (i-start)*ALIGNMENT_PIX_PER_BASE;
- xpos+=(ALIGNMENT_PIX_PER_BASE/2);
- g2.drawLine(xpos, ypos+1, xpos, ypos+5);
- }
--
-+
- if(refSeq != null)
- {
- ypos+=15;
-@@ -3963,7 +3962,7 @@ public class BamView extends JPanel
- }
- }
- }
--
-+
- /**
- * Popup menu listener
- */
-@@ -3973,17 +3972,17 @@ public class BamView extends JPanel
- private JMenuItem showDetails;
- private JMenu coverageMenu;
- private JMenuItem createGroup;
--
-+
- public void mouseClicked(MouseEvent e)
- {
- if(e.isPopupTrigger() ||
- e.getButton() == MouseEvent.BUTTON3)
- return;
--
-+
- BamView.this.requestFocus();
--
-+
- if(e.getClickCount() > 1)
-- getSelection().clear();
-+ getSelection().clear();
- else if(e.getButton() == MouseEvent.BUTTON1)
- {
- if(isCoverageView(getPixPerBaseByWidth()))
-@@ -4017,7 +4016,7 @@ public class BamView extends JPanel
- private void maybeShowPopup(MouseEvent e)
- {
- if(e.isPopupTrigger())
-- {
-+ {
- //
- // main menu options
- if(popup == null)
-@@ -4036,11 +4035,11 @@ public class BamView extends JPanel
- {
- coverageMenu = new JMenu("Coverage HeatMap");
- coverageView.createMenus(coverageMenu);
--
-+
- final JCheckBoxMenuItem coverageGrid = new JCheckBoxMenuItem("Show heatmap grid", false);
- coverageGrid.addActionListener(new ActionListener()
- {
-- public void actionPerformed(ActionEvent e)
-+ public void actionPerformed(ActionEvent e)
- {
- coverageView.showLabels(coverageGrid.isSelected());
- }
-@@ -4051,7 +4050,7 @@ public class BamView extends JPanel
- createGroup.addActionListener(new ActionListener()
- {
- private int n = 1;
-- public void actionPerformed(ActionEvent e)
-+ public void actionPerformed(ActionEvent e)
- {
- String groupName = "group_"+n;
- groupsFrame.addGroup(groupName);
-@@ -4084,7 +4083,7 @@ public class BamView extends JPanel
- thisSAMRecord.sam.getReadName());
- gotoMateMenuItem.addActionListener(new ActionListener()
- {
-- public void actionPerformed(ActionEvent e)
-+ public void actionPerformed(ActionEvent e)
- {
- String name = thisSAMRecord.sam.getMateReferenceName();
- if(name.equals("="))
-@@ -4097,13 +4096,13 @@ public class BamView extends JPanel
- scrollBar.setValue(
- thisSAMRecord.sam.getMateAlignmentStart()+offset-
- (nbasesInView/2));
--
-- highlightSAMRecord = thisSAMRecord;
-- }
-+
-+ highlightSAMRecord = thisSAMRecord;
-+ }
- });
- popup.add(gotoMateMenuItem);
-- }
--
-+ }
-+
- if( mouseOverSAMRecord != null)
- {
- highlightSAMRecord = mouseOverSAMRecord;
-@@ -4145,16 +4144,16 @@ public class BamView extends JPanel
- }
- }
- }
--
-+
- protected static void openFileViewer(SAMRecord readRecord, SAMRecord mateRecord, List<String> bamList)
- {
- FileViewer viewDetail = new FileViewer(readRecord.getReadName(), true, false, false);
- appendToDetailView(readRecord, mateRecord, viewDetail, bamList);
- }
--
-- private static void appendToDetailView(final SAMRecord sam,
-- final SAMRecord mate,
-- final FileViewer viewer,
-+
-+ private static void appendToDetailView(final SAMRecord sam,
-+ final SAMRecord mate,
-+ final FileViewer viewer,
- final List<String> bamList)
- {
- if(bamList.size() > 1 && sam.getAttribute("FL") != null)
-@@ -4163,7 +4162,7 @@ public class BamView extends JPanel
- if(bamIdx < bamList.size())
- viewer.appendString("File "+bamList.get(bamIdx)+"\n\n", Level.INFO);
- }
--
-+
- viewer.appendString("Read Name "+sam.getReadName()+"\n", Level.INFO);
- viewer.appendString("Coordinates "+sam.getAlignmentStart()+".."+
- sam.getAlignmentEnd()+"\n", Level.DEBUG);
-@@ -4176,9 +4175,9 @@ public class BamView extends JPanel
- viewer.appendString("Cigar String "+sam.getCigarString()+"\n", Level.DEBUG);
- viewer.appendString("Strand "+
- (sam.getReadNegativeStrandFlag() ? "-\n\n" : "+\n\n"), Level.DEBUG);
--
-+
- if(sam.getReadPairedFlag())
-- {
-+ {
- if(mate != null)
- {
- viewer.appendString("Mate Coordinates "+mate.getAlignmentStart()+".."+
-@@ -4277,7 +4276,7 @@ public class BamView extends JPanel
- }
- return mate;
- }
--
-+
- protected SAMRecordPredicate getSamRecordFlagPredicate()
- {
- return samRecordFlagPredicate;
-@@ -4290,7 +4289,7 @@ public class BamView extends JPanel
- lastend = -1;
- this.samRecordFlagPredicate = samRecordFlagPredicate;
- }
--
-+
- protected SAMRecordMapQPredicate getSamRecordMapQPredicate()
- {
- return samRecordMapQPredicate;
-@@ -4303,7 +4302,7 @@ public class BamView extends JPanel
- lastend = -1;
- this.samRecordMapQPredicate = samRecordMapQPredicate;
- }
--
-+
- /**
- * @return the concatSequences
- */
-@@ -4332,7 +4331,7 @@ public class BamView extends JPanel
- BamViewRecord sam1;
- BamViewRecord sam2;
- }
--
-+
- class CreateFeatures
- {
- CreateFeatures(final GroupBamFrame groupsFrame)
-@@ -4394,15 +4393,15 @@ public class BamView extends JPanel
- gridPanel.add(cbOpposite, c);
-
- int status =
-- JOptionPane.showConfirmDialog(feature_display, gridPanel,
-+ JOptionPane.showConfirmDialog(feature_display, gridPanel,
- "Options", JOptionPane.OK_CANCEL_OPTION);
- if(status == JOptionPane.CANCEL_OPTION)
- return;
--
-+
- if(!useGroup.isSelected() && minBams.getValue() > bamList.size())
- {
- status =
-- JOptionPane.showConfirmDialog(feature_display,
-+ JOptionPane.showConfirmDialog(feature_display,
- "The minimum number of BAMs setting can not be\n"+
- "greater than the total number of BAM files.\n"+
- "Set this to the number of BAMs (i.e. "+bamList.size()+").",
-@@ -4414,7 +4413,7 @@ public class BamView extends JPanel
- else if(useGroup.isSelected() && minBams.getValue() > groupsFrame.getMaximumBamsInGroup())
- {
- status =
-- JOptionPane.showConfirmDialog(feature_display,
-+ JOptionPane.showConfirmDialog(feature_display,
- "Minimum number of BAMs setting can not be greater than\n"+
- "the total number of BAM files found in any of the groups.\n"+
- "Set this to the greatest number of BAM files in any\n"+
-@@ -4572,7 +4571,7 @@ public class BamView extends JPanel
- boolean covPlot = false;
- boolean snpPlot = false;
- int base = 0;
--
-+
- for(int i=0;i<args.length; i++)
- {
- if(args[i].equals("-a"))
-@@ -4639,7 +4638,7 @@ public class BamView extends JPanel
- final BamView view = new BamView(alignmentFileList, reference, nbasesInView, null, null,
- (JPanel)frame.getContentPane(), frame);
- frame.setTitle("BamView v"+view.getVersion());
--
-+
- if(chr != null)
- view.combo.setSelectedItem(chr);
- if(vw != null)
+ // Iterate through the provided list of features to look at
=====================================
debian/patches/series
=====================================
@@ -1,7 +1,4 @@
-class-path.patch
-jar-rules.patch
-test-classpath.patch
samreader.patch
use-lang3.patch
-build-test.patch
-disable-tests.patch
+#build-test.patch
+#disable-tests.patch
=====================================
debian/patches/use-lang3.patch
=====================================
@@ -2,8 +2,8 @@ Description: use lang3
Author: Sascha Steinbiss
Last-Update: 2016-12-07 23:37:09 +0000
---- a/uk/ac/sanger/artemis/io/GFF3Encoder.java
-+++ b/uk/ac/sanger/artemis/io/GFF3Encoder.java
+--- a/src/main/java/uk/ac/sanger/artemis/io/GFF3Encoder.java
++++ b/src/main/java/uk/ac/sanger/artemis/io/GFF3Encoder.java
@@ -22,7 +22,7 @@
package uk.ac.sanger.artemis.io;
=====================================
debian/rules
=====================================
@@ -35,15 +35,19 @@ CLASSPATH += /usr/share/EMBOSS/jemboss/lib/jemboss.jar \
export CLASSPATH := $(subst $(space),:,$(strip $(CLASSPATH)))
%:
- dh $@ --with javahelper
+ dh $@
-override_dh_auto_build:
+__override_dh_auto_build:
dh_auto_build -- jar
sed 's|@CLASSPATH@|$(subst :,$(space),$(subst $(CURDIR),/usr/share/java/artemis.jar,$(CLASSPATH)))|g' debian/artemis.manifest.in > \
debian/artemis.manifest
- convert images/helix.gif -resize 96x96\! images/helix.png
-override_dh_auto_test:
+override_dh_install:
+ dh_install
+ mkdir -p debian/$(DEB_SOURCE)/usr/share/icons/hicolor/96x96/apps/
+ convert src/main/resources/images/helix.gif -resize 96x96\! debian/$(DEB_SOURCE)/usr/share/icons/hicolor/96x96/apps/helix.png
+
+__override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
ln -s /usr/share/javascript/jquery/jquery.js test/coverage-report/evosuite-auto-tests/files/jquery.js
ln -s /usr/share/javascript/jquery/jquery.js test/coverage-report/evosuite-auto-tests/html/files/jquery.js
@@ -53,7 +57,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
rm test/coverage-report/evosuite-auto-tests/files/jquery.js test/coverage-report/evosuite-auto-tests/html/files/jquery.js
endif
-override_dh_auto_clean:
+__override_dh_auto_clean:
dh_auto_clean
$(RM) debian/artemis.manifest
$(RM) images/helix.png
=====================================
debian/upstream/edam
=====================================
@@ -7,10 +7,10 @@ scopes:
function:
- Genome visualisation
- Genome annotation
- inputs:
+ input:
- data: Sequence
formats: [BAM, FASTA, GFF, EMBL format, VCF, BCF]
- outputs:
+ output:
- data: Sequence
formats: [GFF, EMBL format, FASTA, GenBank format]
- data: Sequence image
View it on GitLab: https://salsa.debian.org/med-team/artemis/commit/bc46cc86da3873bd0aba46d09796fc664048f23f
--
View it on GitLab: https://salsa.debian.org/med-team/artemis/commit/bc46cc86da3873bd0aba46d09796fc664048f23f
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