[Debian-med-packaging] [SCM] igv branch, master, updated. upstream/1.4.2-5-g3f90e19

[Shaun Jackman]

The following commit has been merged in the master branch:
commit 3f90e19830dfdc4f96a4d92610eaef3240880dab
Author: Shaun Jackman <sjackman at debian.org>
Date:   Thu Jun 17 16:50:37 2010 -0700

    * build.xml: Remove maf.jar.
    * src/org/broad/igv/track/TrackManager.java: Remove support for MAF files.
    * src/org/broad/igv/PreferenceManager.java: Ditto.

diff --git a/debian/patches/debian-changes-1.4.2-1 b/debian/patches/debian-changes-1.4.2-1
index e3bc352..d176a3f 100644
--- a/debian/patches/debian-changes-1.4.2-1
+++ b/debian/patches/debian-changes-1.4.2-1
@@ -34,7 +34,7 @@ Last-Update: <YYYY-MM-DD>
  
      <!-- Platform specific input files -->
      <property name="native.dir"        value="${basedir}/native/" />
-@@ -54,27 +54,25 @@
+@@ -54,27 +54,24 @@
          <!-- Create class path for manifest -->
          <path id="@jars">
              <pathelement path="${lib.dir}AbsoluteLayout.jar" />
@@ -59,15 +59,46 @@ Last-Update: <YYYY-MM-DD>
              <pathelement path="${lib.dir}jlfgr-1_0.jar" />
              <pathelement path="${lib.dir}ledatastream.jar" />
 -            <pathelement path="${lib.dir}log4j-1.2.15.jar" />
-+            <pathelement path="${lib.dir}log4j-1.2.jar" />
-             <pathelement path="${lib.dir}maf.jar" />
+-            <pathelement path="${lib.dir}maf.jar" />
 -            <pathelement path="${lib.dir}sam-1.08.jar" />
 -            <pathelement path="${lib.dir}swing-layout-1.0.jar" />
++            <pathelement path="${lib.dir}log4j-1.2.jar" />
 +            <pathelement path="${lib.dir}sam.jar" />
 +            <pathelement path="${lib.dir}swing-layout.jar" />
          </path>
  
          <pathconvert property="class-path" pathsep=" " dirsep="/" refid="@jars">
+@@ -105,7 +102,7 @@
+     </target>
+ 
+     <target name="compile" depends="init">
+-        <javac srcdir="${src.dir}"  debug="on" destdir="${tmp.dir}">
++        <javac srcdir="${src.dir}" excludes="org/broad/igv/maf/*" debug="on" destdir="${tmp.dir}">
+             <classpath refid="@jars" />
+         </javac>
+     </target>
+--- igv-1.4.2.orig/src/org/broad/igv/PreferenceManager.java
++++ igv-1.4.2/src/org/broad/igv/PreferenceManager.java
+@@ -25,7 +25,9 @@ package org.broad.igv;
+ 
+ import org.apache.log4j.Logger;
+ import org.broad.igv.feature.Mutation;
++/*
+ import org.broad.igv.maf.MAFManager;
++*/
+ import org.broad.igv.renderer.ColorScaleFactory;
+ import org.broad.igv.renderer.ContinuousColorScale;
+ import org.broad.igv.track.TrackType;
+@@ -305,7 +307,9 @@ public class PreferenceManager implement
+ 
+         String[] species = null;
+         if (tmp == null) {
++/*
+             species = MAFManager.species;
++*/
+         } else {
+             species = tmp.split(":");
+         }
 --- igv-1.4.2.orig/src/org/broad/igv/h5/HDF5LocalWriter.java
 +++ igv-1.4.2/src/org/broad/igv/h5/HDF5LocalWriter.java
 @@ -491,7 +491,7 @@ public class HDF5LocalWriter implements
@@ -79,6 +110,49 @@ Last-Update: <YYYY-MM-DD>
                  buf =
                          value.toString().getBytes();
                  H5.H5Tset_size(dataType, ((byte[]) buf).length);
+--- igv-1.4.2.orig/src/org/broad/igv/track/TrackManager.java
++++ igv-1.4.2/src/org/broad/igv/track/TrackManager.java
+@@ -34,9 +34,11 @@ import org.broad.igv.data.rnai.RNAIHairp
+ import org.broad.igv.exceptions.DataLoadException;
+ import org.broad.igv.feature.*;
+ import org.broad.igv.feature.dranger.DRangerParser;
++/*
+ import org.broad.igv.maf.MAFTrack;
+ import org.broad.igv.maf.conservation.OmegaDataSource;
+ import org.broad.igv.maf.conservation.OmegaTrack;
++*/
+ import org.broad.igv.renderer.DASFeatureRenderer;
+ import org.broad.igv.renderer.GeneTrackRenderer;
+ import org.broad.igv.renderer.HeatmapRenderer;
+@@ -820,10 +822,12 @@ public class TrackManager {
+                     typeString.endsWith(".aligned") || typeString.endsWith(".sai") ||
+                     typeString.endsWith(".bai") || typeString.endsWith(".bedz")) {
+                 loadAlignmentsTrack(locator, newTracks);
++/*
+             } else if (typeString.endsWith(".maf")) {
+                 loadMAFTrack(locator, newTracks);
+             } else if (typeString.endsWith("omega")) {
+                 loadOmegaTrack(locator, newTracks);
++*/
+             } else if (typeString.endsWith("wig")) {
+                 loadWigFile(locator, newTracks);
+             } else if (typeString.endsWith("list")) {
+@@ -1299,6 +1303,7 @@ public class TrackManager {
+         (new RNAIHairpinParser(locator.getPath())).parse();
+     }
+ 
++/*
+     private void loadMAFTrack(ResourceLocator locator, List<Track> newTracks) {
+ 
+         MAFTrack t = new MAFTrack(locator, "Multiple Alignments");
+@@ -1315,6 +1320,7 @@ public class TrackManager {
+         //track.setDataRange(new DataRange(-3, 0, 3));
+         newTracks.add(track);
+     }
++*/
+ 
+     /**
+      * Load a rnai gene score file and create a datasource and track.
 --- igv-1.4.2.orig/src/org/broad/igv/ui/util/GenericUtilities.java
 +++ igv-1.4.2/src/org/broad/igv/ui/util/GenericUtilities.java
 @@ -27,7 +27,7 @@ package org.broad.igv.ui.util;

-- 
Integrative Genomics Viewer