[Git][java-team/openchemlib][master] 4 commits: New upstream version 2020.12.1+dfsg
Andrius Merkys
gitlab at salsa.debian.org
Mon Dec 14 12:45:19 GMT 2020
Andrius Merkys pushed to branch master at Debian Java Maintainers / openchemlib
Commits:
b6db7476 by Andrius Merkys at 2020-12-14T02:52:08-05:00
New upstream version 2020.12.1+dfsg
- - - - -
81b70ed0 by Andrius Merkys at 2020-12-14T02:52:39-05:00
Update upstream source from tag 'upstream/2020.12.1+dfsg'
Update to upstream version '2020.12.1+dfsg'
with Debian dir b5f8865328a03fd49930f20650109924d1aca47c
- - - - -
7db1032f by Andrius Merkys at 2020-12-14T03:06:04-05:00
Refreshing patches.
- - - - -
a7fd213e by Andrius Merkys at 2020-12-14T03:06:22-05:00
Update changelog for 2020.12.1+dfsg-1 release
- - - - -
11 changed files:
- debian/changelog
- debian/patches/javafx.patch
- debian/patches/libtablelayout-java.patch
- pom.xml
- src/main/java/com/actelion/research/chem/AromaticityResolver.java
- src/main/java/com/actelion/research/chem/ExtendedMolecule.java
- src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java
- src/main/java/com/actelion/research/chem/Molecule.java
- src/main/java/com/actelion/research/chem/io/CompoundTableConstants.java
- src/main/java/com/actelion/research/gui/CompoundCollectionPane.java
- + src/main/java/com/actelion/research/gui/ScrollPaneAutoScrollerWhenDragging.java
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+openchemlib (2020.12.1+dfsg-1) unstable; urgency=medium
+
+ * New upstream version 2020.12.1+dfsg
+ * Refreshing patches.
+
+ -- Andrius Merkys <merkys at debian.org> Mon, 14 Dec 2020 03:06:17 -0500
+
openchemlib (2020.12.0+dfsg-1) unstable; urgency=medium
* New upstream version 2020.12.0+dfsg
=====================================
debian/patches/javafx.patch
=====================================
@@ -1,6 +1,6 @@
--- a/pom.xml
+++ b/pom.xml
-@@ -101,6 +101,21 @@
+@@ -107,6 +107,21 @@
<version>4.13.1</version>
<scope>test</scope>
</dependency>
=====================================
debian/patches/libtablelayout-java.patch
=====================================
@@ -1,6 +1,6 @@
--- a/pom.xml
+++ b/pom.xml
-@@ -116,6 +116,10 @@
+@@ -122,6 +122,10 @@
<artifactId>javafx-graphics</artifactId>
<version>11</version>
</dependency>
=====================================
pom.xml
=====================================
@@ -8,7 +8,7 @@
Please follow the naming scheme YEAR.MONTH.RELEASE_NO_OF_MONTH
(eg. 2016.4.1 for second release in Apr 2016)
-->
- <version>2020.12.0</version>
+ <version>2020.12.1</version>
<name>OpenChemLib</name>
<description>Open Source Chemistry Library</description>
@@ -195,7 +195,7 @@
<connection>scm:git:git at github.com:Actelion/openchemlib.git</connection>
<developerConnection>scm:git:git at github.com:Actelion/openchemlib.git</developerConnection>
<url>https://github.com/Actelion/openchemlib</url>
- <tag>openchemlib-2020.12.0</tag>
+ <tag>openchemlib-2020.12.1</tag>
</scm>
<distributionManagement>
=====================================
src/main/java/com/actelion/research/chem/AromaticityResolver.java
=====================================
@@ -672,28 +672,34 @@ public class AromaticityResolver {
private boolean checkAtomTypePi1(int atom, boolean correctCharge) {
int atomicNo = mMol.getAtomicNo(atom);
if ((atomicNo >=5 && atomicNo <= 8)
- || atomicNo == 15 || atomicNo == 16 || atomicNo == 33 || atomicNo == 34) { // P,S,As,Se
- int freeValence = mMol.getFreeValence(atom);
- if (freeValence == 1 || freeValence == 2) // we allow one more free valence, because the atom may have a missing charge
+ || atomicNo == 15 || atomicNo == 16 || atomicNo == 33 || atomicNo == 34 || atomicNo == 52) { // P,S,As,Se,Te
+
+// Old logic seems fishy to me; TLS 10Dec2020
+// int freeValence = mMol.getFreeValence(atom);
+// if (freeValence == 1 || freeValence == 2) // we allow one more free valence, because the atom may have a missing charge
+// return true;
+
+ int freeValence = mMol.getLowestFreeValence(atom);
+ if (freeValence != 0)
return true;
if (mMol.getAtomCharge(atom) == 0) {
- if ((atomicNo == 15 || atomicNo == 33) && freeValence == 3) {
+ if ((atomicNo == 15 || atomicNo == 33) /* && freeValence == 3 */) {
if (correctCharge)
mMol.setAtomCharge(atom, 1);
return true;
}
- if ((atomicNo == 16 || atomicNo == 34) && freeValence == 4) {
+ if ((atomicNo == 16 || atomicNo == 34 || atomicNo == 52) /* && freeValence == 4 */) {
if (correctCharge)
mMol.setAtomCharge(atom, 1);
return true;
}
- if (atomicNo == 5 && freeValence == 0) {
+ if (atomicNo == 5 /* && freeValence == 0 */) {
if (correctCharge)
mMol.setAtomCharge(atom, -1);
return true;
}
- if ((atomicNo == 7 || atomicNo == 8) && freeValence == 0) {
+ if ((atomicNo == 7 || atomicNo == 8) /* && freeValence == 0 */) {
if (correctCharge)
mMol.setAtomCharge(atom, 1);
return true;
@@ -725,7 +731,7 @@ public class AromaticityResolver {
if (mMol.getConnAtoms(atom) == 3)
return 8;
}
- else if (mMol.getAtomicNo(atom) == 16 || mMol.getAtomicNo(atom) == 34) {
+ else if (mMol.getAtomicNo(atom) == 16 || mMol.getAtomicNo(atom) == 34 || mMol.getAtomicNo(atom) == 52) {
if (mMol.getConnAtoms(atom) == 2)
return 12;
}
=====================================
src/main/java/com/actelion/research/chem/ExtendedMolecule.java
=====================================
@@ -548,7 +548,7 @@ public class ExtendedMolecule extends Molecule implements Serializable {
/**
- * The free valence is the number of potential additional single bonded
+ * The lowest free valence is the number of potential additional single bonded
* neighbours to reach the atom's lowest valence above or equal its current
* occupied valence. Atom charges are considered. Implicit hydrogens are not considered.
* Thus, the phosphor atoms in PF2 and PF4 both have a lowest free valence of 1.
=====================================
src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java
=====================================
@@ -957,20 +957,24 @@ public class IDCodeParserWithoutCoordinateInvention {
}
public boolean coordinatesAre3D(byte[] idcode, byte[] coordinates) {
- if (coordinates == null || coordinates.length == 0)
+ return coordinatesAre3D(idcode, coordinates, 0, 0);
+ }
+
+ public boolean coordinatesAre3D(byte[] idcode, byte[] coordinates, int idcodeStart, int coordsStart) {
+ if (coordinates == null || coordinates.length <= coordsStart)
return false;
- if (coordinates[0] == '!' || coordinates[0] == '#') {
+ if (coordinates[coordsStart] == '!' || coordinates[coordsStart] == '#') {
// current version starts with '!' (ASC 33) or '#' (ASC 35) (includs implicit hydrogen coordinates)
// further versions may start with ASC 36 to 38
- decodeBitsStart(coordinates, 1);
+ decodeBitsStart(coordinates, coordsStart+1);
return (decodeBits(1) == 1);
}
else { // old format uses ACSII 39 and higher
- int allAtoms = getAtomCount(idcode, 0);
+ int allAtoms = getAtomCount(idcode, idcodeStart);
return (allAtoms != 0
- && coordinates.length >= 3*allAtoms-3
- && coordinates[2*allAtoms-2] != '\'');
+ && coordinates.length >= coordsStart+3*allAtoms-3
+ && coordinates[coordsStart+2*allAtoms-2] != '\'');
}
}
=====================================
src/main/java/com/actelion/research/chem/Molecule.java
=====================================
@@ -3775,6 +3775,7 @@ public class Molecule implements Serializable {
case 33: // As
case 34: // Se
case 35: // Br
+ case 52: // Te
case 53: // I
return true;
}
=====================================
src/main/java/com/actelion/research/chem/io/CompoundTableConstants.java
=====================================
@@ -91,7 +91,7 @@ public interface CompoundTableConstants {
int cStructureHiliteModeFilter = 0;
int cStructureHiliteModeCurrentRow = 1;
int cStructureHiliteModeNone = 2;
- String[] cStructureHiliteModeText = { "Most Recent Filter", "Current Row Similarity", "No Highlighting" };
+ String[] cStructureHiliteModeText = { "Most Recent Filter", "Similarity To Reference Row", "No Highlighting" };
String[] cStructureHiliteModeCode = { "hiliteFilter", "hiliteCurrent", "hiliteNone" };
// highlight mode for part-of-reaction highlighting depending on current record similarity
=====================================
src/main/java/com/actelion/research/gui/CompoundCollectionPane.java
=====================================
@@ -79,6 +79,8 @@ public class CompoundCollectionPane<T> extends JScrollPane
private JPanel mContentPanel;
private boolean mIsVertical,mIsEditable,mIsSelectable,mCreateFragments,
mIsEnabled,mShowValidationError,mInternalDragAndDropIsMove;
+ private ScrollPaneAutoScrollerWhenDragging mScroller;
+
/**
* This is a visual component to display and edit a compound collection maintained
@@ -108,6 +110,7 @@ public class CompoundCollectionPane<T> extends JScrollPane
mDropIndex = -1;
init();
initializeDragAndDrop(dragAction, dropAction);
+ mScroller = new ScrollPaneAutoScrollerWhenDragging(this, isVertical);
}
public CompoundCollectionModel<T> getModel() {
@@ -424,7 +427,7 @@ public class CompoundCollectionPane<T> extends JScrollPane
g.drawString("?", bounds.x+(bounds.width-(int)b.getWidth())/2, bounds.y+(bounds.height-(int)b.getHeight())/2+m.getAscent());
}
}
-
+
Depictor2D d = new Depictor2D(compound, mDisplayMode);
d.validateView(g,
new Rectangle2D.Double(bounds.x, bounds.y, bounds.width, bounds.height),
@@ -706,6 +709,7 @@ public class CompoundCollectionPane<T> extends JScrollPane
@Override
public void dragOver(DropTargetDragEvent e) {
+ mScroller.autoScroll();
updateDropPosition(getDropIndex(e));
}
=====================================
src/main/java/com/actelion/research/gui/ScrollPaneAutoScrollerWhenDragging.java
=====================================
@@ -0,0 +1,73 @@
+package com.actelion.research.gui;
+
+import com.actelion.research.gui.hidpi.HiDPIHelper;
+
+import javax.swing.*;
+import java.awt.*;
+
+public class ScrollPaneAutoScrollerWhenDragging {
+ private static final int SCROLL_AREA_HEIGHT = HiDPIHelper.scale(32);
+ private static final int SCROLL_SLEEP_MILLIS = 20;
+ private static final int SCROLL_MAX_PIXELS = HiDPIHelper.scale(16);
+
+ private JScrollPane mScrollPane;
+ private boolean mIsVertical;
+ private int mContentSize,mViewportSize;
+ private Thread mScrollThread;
+ private float mScrollSpeed;
+
+ public ScrollPaneAutoScrollerWhenDragging(JScrollPane scrollPane, boolean isVertical) {
+ mScrollPane = scrollPane;
+ mIsVertical = isVertical;
+ }
+
+ public void autoScroll() {
+ Component content = mScrollPane.getViewport().getView();
+ mContentSize = mIsVertical ? content.getHeight() : content.getWidth();
+ mViewportSize = mIsVertical ? mScrollPane.getViewport().getHeight() : mScrollPane.getViewport().getWidth();
+
+ Point mp = mScrollPane.getMousePosition();
+ if (mp != null) {
+ int mousePosition = mIsVertical ? mp.y : mp.x;
+ int viewportPosition = mIsVertical ? mScrollPane.getViewport().getY() : mScrollPane.getViewport().getX();
+ int mouseToTop = mousePosition - viewportPosition;
+ int mouseToBottom = viewportPosition + mViewportSize - mousePosition;
+ mScrollSpeed = (mouseToTop < SCROLL_AREA_HEIGHT) ? -Math.min(1.0f, (float) (SCROLL_AREA_HEIGHT - mouseToTop) / SCROLL_AREA_HEIGHT)
+ : (mouseToBottom < SCROLL_AREA_HEIGHT) ? Math.min(1.0f, (float) (SCROLL_AREA_HEIGHT - mouseToBottom) / SCROLL_AREA_HEIGHT) : 0;
+ }
+
+ if (mScrollSpeed == 0) {
+ mScrollThread = null;
+ }
+ else if (mScrollThread == null) {
+ mScrollThread = new Thread(() -> {
+ while (mScrollThread != null) {
+ Point vp = mScrollPane.getViewport().getViewPosition();
+ int minStep = mIsVertical ? -vp.y : -vp.x;
+ int maxStep = Math.max(0, mContentSize - mViewportSize + minStep);
+ int step = Math.max(minStep, Math.min(maxStep, Math.round(mScrollSpeed * SCROLL_MAX_PIXELS)));
+ if (step == 0) {
+ mScrollThread = null;
+ }
+ else {
+ if (mIsVertical)
+ vp.y += step;
+ else
+ vp.x += step;
+ try {
+//System.out.println("Thread:"+mScrollThread+" auto-scrolling:"+step);
+ SwingUtilities.invokeAndWait(() -> mScrollPane.getViewport().setViewPosition(vp));
+ Thread.sleep(SCROLL_SLEEP_MILLIS);
+ }
+ catch (Exception ie) {}
+ }
+ }
+ });
+ mScrollThread.start();
+ }
+ }
+
+ public void stopScrolling() {
+ mScrollThread = null;
+ }
+ }
View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/compare/c1316dfc3459d1af730a8dbceb79f5a32377fce3...a7fd213ee0b1ef8a3a5c279a138bd0673368829e
--
View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/compare/c1316dfc3459d1af730a8dbceb79f5a32377fce3...a7fd213ee0b1ef8a3a5c279a138bd0673368829e
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/pkg-java-commits/attachments/20201214/bacda2a8/attachment.html>
More information about the pkg-java-commits
mailing list