X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=8cad9ca474c857d83eb3ba0e8536e4fc249cea35;hb=c2214808f64b811a25cec10399dcff38db0c592c;hp=3bca941fc3f8a30988b197327cf14942b1a0dc87;hpb=baaf65b19f3dfea486da401fba610ac66bf36817;p=jalview.git
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3bca941..8cad9ca 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -279,7 +281,7 @@ public class Jalview2XML
return;
}
- Hashtable dsses = new Hashtable();
+ Hashtable dsses = new Hashtable();
try
{
@@ -348,7 +350,8 @@ public class Jalview2XML
SaveState(apanel, fileName, jout);
- String dssid = getDatasetIdRef(af.getViewport().getAlignment().getDataset());
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
if (!dsses.containsKey(dssid))
{
dsses.put(dssid, af);
@@ -358,8 +361,9 @@ public class Jalview2XML
}
}
- writeDatasetFor(dsses, ""+jout.hashCode()+" "+uniqueSetSuffix, jout);
-
+ writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
+ jout);
+
try
{
jout.flush();
@@ -389,7 +393,7 @@ public class Jalview2XML
int ap, apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
- Hashtable dsses = new Hashtable();
+ Hashtable dsses = new Hashtable();
for (ap = 0; ap < apSize; ap++)
{
AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
@@ -400,7 +404,8 @@ public class Jalview2XML
jfileName = jfileName + ".xml";
}
SaveState(apanel, jfileName, jout);
- String dssid = getDatasetIdRef(af.getViewport().getAlignment().getDataset());
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
if (!dsses.containsKey(dssid))
{
dsses.put(dssid, af);
@@ -428,10 +433,10 @@ public class Jalview2XML
String fileName, JarOutputStream jout)
{
- for (String dssids:dsses.keySet())
+ for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
- String jfileName = fileName + " Dataset for "+ _af.getTitle();
+ String jfileName = fileName + " Dataset for " + _af.getTitle();
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
@@ -456,25 +461,27 @@ public class Jalview2XML
public JalviewModel SaveState(AlignmentPanel ap, String fileName,
JarOutputStream jout)
{
- return SaveState(ap, fileName, false,jout);
+ return SaveState(ap, fileName, false, jout);
}
+
/**
- * create a JalviewModel from an algnment view and marshall it to a
- * JarOutputStream
- *
- * @param ap
- * panel to create jalview model for
- * @param fileName
- * name of alignment panel written to output stream
- * @param storeDS
- * when true, only write the dataset for the alignment, not the data associated with the view.
- * @param jout
- * jar output stream
- * @param out
- * jar entry name
- */
- public JalviewModel SaveState(AlignmentPanel ap, String fileName, boolean storeDS,
- JarOutputStream jout)
+ * create a JalviewModel from an algnment view and marshall it to a
+ * JarOutputStream
+ *
+ * @param ap
+ * panel to create jalview model for
+ * @param fileName
+ * name of alignment panel written to output stream
+ * @param storeDS
+ * when true, only write the dataset for the alignment, not the data
+ * associated with the view.
+ * @param jout
+ * jar output stream
+ * @param out
+ * jar entry name
+ */
+ public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+ boolean storeDS, JarOutputStream jout)
{
initSeqRefs();
Vector jmolViewIds = new Vector(); //
@@ -486,7 +493,8 @@ public class Jalview2XML
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- object.setVersion(jalview.bin.Cache.getDefault("VERSION","Development Build"));
+ object.setVersion(jalview.bin.Cache.getDefault("VERSION",
+ "Development Build"));
jalview.datamodel.AlignmentI jal = av.getAlignment();
@@ -529,11 +537,12 @@ public class Jalview2XML
// SAVE SEQUENCES
String id = "";
- jalview.datamodel.SequenceI jds,jdatasq;
+ jalview.datamodel.SequenceI jds, jdatasq;
for (int i = 0; i < jal.getHeight(); i++)
{
jds = jal.getSequenceAt(i);
- jdatasq=jds.getDatasetSequence() == null ? jds : jds.getDatasetSequence();
+ jdatasq = jds.getDatasetSequence() == null ? jds : jds
+ .getDatasetSequence();
id = seqHash(jds);
if (seqRefIds.get(id) != null)
@@ -877,17 +886,19 @@ public class Jalview2XML
IdentityHashMap groupRefs = new IdentityHashMap();
if (storeDS)
{
- for (SequenceI sq:jal.getSequences())
+ for (SequenceI sq : jal.getSequences())
+ {
+ // Store annotation on dataset sequences only
+ jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation();
+ if (aa != null && aa.length > 0)
{
- // Store annotation on dataset sequences only
- jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation();
- if (aa!=null && aa.length>0)
- {
- storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
- vamsasSet);
- }
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
}
- } else {
+ }
+ }
+ else
+ {
if (jal.getAlignmentAnnotation() != null)
{
// Store the annotation shown on the alignment.
@@ -933,10 +944,10 @@ public class Jalview2XML
}
else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
{
- groups[i]
- .setColour(ColourSchemeProperty
- .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
- .getBaseColour()));
+ groups[i].setColour("AnnotationColourGradient");
+ groups[i].setAnnotationColours(constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) sg.cs,
+ userColours, jms));
}
else if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
@@ -1009,28 +1020,11 @@ public class Jalview2XML
}
else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
{
- jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
- .getGlobalColourScheme();
+ AnnotationColours ac = constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) av
+ .getGlobalColourScheme(),
+ userColours, jms);
- AnnotationColours ac = new AnnotationColours();
- ac.setAboveThreshold(acg.getAboveThreshold());
- ac.setThreshold(acg.getAnnotationThreshold());
- ac.setAnnotation(acg.getAnnotation());
- if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
- {
- ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
- userColours, jms));
- }
- else
- {
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg
- .getBaseColour()));
- }
-
- ac.setMaxColour(acg.getMaxColour().getRGB());
- ac.setMinColour(acg.getMinColour().getRGB());
- ac.setPerSequence(acg.isSeqAssociated());
- ac.setPredefinedColours(acg.isPredefinedColours());
view.setAnnotationColours(ac);
view.setBgColour("AnnotationColourGradient");
}
@@ -1250,7 +1244,35 @@ public class Jalview2XML
return object;
}
- private void storeAlignmentAnnotation(AlignmentAnnotation[] aa, IdentityHashMap groupRefs, AlignmentViewport av, Set calcIdSet, boolean storeDS, SequenceSet vamsasSet)
+ private AnnotationColours constructAnnotationColours(
+ AnnotationColourGradient acg, Vector userColours,
+ JalviewModelSequence jms)
+ {
+ AnnotationColours ac = new AnnotationColours();
+ ac.setAboveThreshold(acg.getAboveThreshold());
+ ac.setThreshold(acg.getAnnotationThreshold());
+ ac.setAnnotation(acg.getAnnotation());
+ if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ {
+ ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+ userColours, jms));
+ }
+ else
+ {
+ ac.setColourScheme(ColourSchemeProperty.getColourName(acg
+ .getBaseColour()));
+ }
+
+ ac.setMaxColour(acg.getMaxColour().getRGB());
+ ac.setMinColour(acg.getMinColour().getRGB());
+ ac.setPerSequence(acg.isSeqAssociated());
+ ac.setPredefinedColours(acg.isPredefinedColours());
+ return ac;
+ }
+
+ private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
+ IdentityHashMap groupRefs, AlignmentViewport av,
+ Set calcIdSet, boolean storeDS, SequenceSet vamsasSet)
{
for (int i = 0; i < aa.length; i++)
@@ -1382,11 +1404,12 @@ public class Jalview2XML
}
if (!storeDS || (storeDS && !aa[i].autoCalculated))
{
- // skip autocalculated annotation - these are only provided for alignments
+ // skip autocalculated annotation - these are only provided for
+ // alignments
vamsasSet.addAnnotation(an);
}
}
-
+
}
private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
@@ -1772,7 +1795,7 @@ public class Jalview2XML
try
{
// create list to store references for any new Jmol viewers created
- newStructureViewers=new Vector();
+ newStructureViewers = new Vector();
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
@@ -1780,13 +1803,13 @@ public class Jalview2XML
jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
af = LoadJalviewAlign(jprovider);
-
+
} catch (MalformedURLException e)
{
errorMessage = "Invalid URL format for '" + file + "'";
reportErrors();
- }
- finally {
+ } finally
+ {
try
{
SwingUtilities.invokeAndWait(new Runnable()
@@ -1872,7 +1895,7 @@ public class Jalview2XML
frefedSequence = new Vector();
}
- jalview.gui.AlignFrame af= null,_af = null;
+ jalview.gui.AlignFrame af = null, _af = null;
Hashtable gatherToThisFrame = new Hashtable();
final String file = jprovider.getFilename();
try
@@ -1903,8 +1926,7 @@ public class Jalview2XML
if (object.getJalviewModelSequence().getViewportCount() > 0)
{
af = _af;
- if (object.getJalviewModelSequence().getViewportCount() > 1
- && af.viewport.gatherViewsHere)
+ if (af.viewport.gatherViewsHere)
{
gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
}
@@ -2130,8 +2152,9 @@ public class Jalview2XML
JalviewModelSequence jms = object.getJalviewModelSequence();
- Viewport view = (jms.getViewportCount()>0) ? jms.getViewport(0) : null;
-
+ Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
+ : null;
+
// ////////////////////////////////
// LOAD SEQUENCES
@@ -2537,14 +2560,13 @@ public class Jalview2XML
}
}
}
-
// ///////////////////////
// LOAD GROUPS
// Create alignment markup and styles for this view
if (jms.getJGroupCount() > 0)
{
JGroup[] groups = jms.getJGroup();
-
+ boolean addAnnotSchemeGroup = false;
for (int i = 0; i < groups.length; i++)
{
ColourSchemeI cs = null;
@@ -2555,6 +2577,12 @@ public class Jalview2XML
{
cs = GetUserColourScheme(jms, groups[i].getColour());
}
+ else if (groups[i].getColour().equals("AnnotationColourGradient")
+ && groups[i].getAnnotationColours() != null)
+ {
+ addAnnotSchemeGroup = true;
+ cs = null;
+ }
else
{
cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
@@ -2653,10 +2681,15 @@ public class Jalview2XML
}
}
al.addGroup(sg);
-
+ if (addAnnotSchemeGroup)
+ {
+ // reconstruct the annotation colourscheme
+ sg.cs = constructAnnotationColour(
+ groups[i].getAnnotationColours(), null, al, jms, false);
+ }
}
}
- if (view==null)
+ if (view == null)
{
// only dataset in this model, so just return.
return null;
@@ -2704,6 +2737,13 @@ public class Jalview2XML
}
}
+ /**
+ * indicate that annotation colours are applied across all groups (pre
+ * Jalview 2.8.1 behaviour)
+ */
+ boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
+ object.getVersion());
+
AlignmentPanel ap = null;
boolean isnewview = true;
if (viewId != null)
@@ -3168,25 +3208,84 @@ public class Jalview2XML
// and finally return.
return af;
}
- Vector newStructureViewers=null;
+
+ /**
+ *
+ * @param supported
+ * - minimum version we are comparing against
+ * @param version
+ * - version of data being processsed.
+ * @return true if version is development/null or evaluates to the same or
+ * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
+ */
+ private boolean isVersionStringLaterThan(String supported, String version)
+ {
+ if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
+ || version.equalsIgnoreCase("Test")
+ || version.equalsIgnoreCase("AUTOMATED BUILD"))
+ {
+ System.err.println("Assuming project file with "
+ + (version == null ? "null" : version)
+ + " is compatible with Jalview version " + supported);
+ return true;
+ }
+ else
+ {
+ StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer(
+ version, ".");
+ while (currentV.hasMoreTokens() && fileV.hasMoreTokens())
+ {
+ // convert b to decimal to catch bugfix releases within a series
+ String curT = currentV.nextToken().toLowerCase().replace('b', '.');
+ String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
+ try
+ {
+ if (Float.valueOf(curT) > Float.valueOf(fileT))
+ {
+ // current version is newer than the version that wrote the file
+ return false;
+ }
+ } catch (NumberFormatException nfe)
+ {
+ System.err
+ .println("** WARNING: Version comparison failed for tokens ("
+ + curT
+ + ") and ("
+ + fileT
+ + ")\n** Current: '"
+ + supported + "' and Version: '" + version + "'");
+ }
+ }
+ if (currentV.hasMoreElements())
+ {
+ // fileV has no minor version but identical series to current
+ return false;
+ }
+ }
+ return true;
+ }
+
+ Vector newStructureViewers = null;
+
protected void addNewStructureViewer(AppJmol sview)
{
- if (newStructureViewers!=null)
+ if (newStructureViewers != null)
{
sview.jmb.setFinishedLoadingFromArchive(false);
newStructureViewers.add(sview);
}
}
+
protected void setLoadingFinishedForNewStructureViewers()
{
- if (newStructureViewers!=null)
+ if (newStructureViewers != null)
{
- for (AppJmol sview:newStructureViewers)
+ for (AppJmol sview : newStructureViewers)
{
sview.jmb.setFinishedLoadingFromArchive(true);
}
newStructureViewers.clear();
- newStructureViewers=null;
+ newStructureViewers = null;
}
}
@@ -3303,111 +3402,11 @@ public class Jalview2XML
}
else if (view.getBgColour().startsWith("Annotation"))
{
- // int find annotation
- if (af.viewport.getAlignment().getAlignmentAnnotation() != null)
- {
- for (int i = 0; i < af.viewport.getAlignment()
- .getAlignmentAnnotation().length; i++)
- {
- if (af.viewport.getAlignment().getAlignmentAnnotation()[i].label
- .equals(view.getAnnotationColours().getAnnotation()))
- {
- if (af.viewport.getAlignment().getAlignmentAnnotation()[i]
- .getThreshold() == null)
- {
- af.viewport.getAlignment().getAlignmentAnnotation()[i]
- .setThreshold(new jalview.datamodel.GraphLine(view
- .getAnnotationColours().getThreshold(),
- "Threshold", java.awt.Color.black)
-
- );
- }
+ AnnotationColours viewAnnColour = view.getAnnotationColours();
+ cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
- if (view.getAnnotationColours().getColourScheme()
- .equals("None"))
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- new java.awt.Color(view.getAnnotationColours()
- .getMinColour()), new java.awt.Color(view
- .getAnnotationColours().getMaxColour()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else if (view.getAnnotationColours().getColourScheme()
- .startsWith("ucs"))
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- GetUserColourScheme(jms, view
- .getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al, view
- .getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold());
- }
- if (view.getAnnotationColours().hasPerSequence())
- {
- ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
- }
- if (view.getAnnotationColours().hasPredefinedColours())
- {
- ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
- }
- // Also use these settings for all the groups
- if (al.getGroups() != null)
- {
- for (int g = 0; g < al.getGroups().size(); g++)
- {
- jalview.datamodel.SequenceGroup sg = al.getGroups()
- .get(g);
-
- if (sg.cs == null)
- {
- continue;
- }
+ // annpos
- /*
- * if
- * (view.getAnnotationColours().getColourScheme().equals("None"
- * )) { sg.cs = new AnnotationColourGradient(
- * af.viewport.getAlignment().getAlignmentAnnotation()[i], new
- * java.awt.Color(view.getAnnotationColours().
- * getMinColour()), new
- * java.awt.Color(view.getAnnotationColours().
- * getMaxColour()),
- * view.getAnnotationColours().getAboveThreshold()); } else
- */
- {
- sg.cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- sg.cs, view.getAnnotationColours()
- .getAboveThreshold());
- if (cs instanceof AnnotationColourGradient)
- {
- if (view.getAnnotationColours().hasPerSequence())
- {
- ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
- }
- if (view.getAnnotationColours().hasPredefinedColours())
- {
- ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
- }
- }
- }
-
- }
- }
-
- break;
- }
-
- }
- }
}
else
{
@@ -3601,6 +3600,131 @@ public class Jalview2XML
return af;
}
+ private ColourSchemeI constructAnnotationColour(
+ AnnotationColours viewAnnColour, AlignFrame af, Alignment al,
+ JalviewModelSequence jms, boolean checkGroupAnnColour)
+ {
+ boolean propagateAnnColour = false;
+ ColourSchemeI cs = null;
+ AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
+ if (checkGroupAnnColour && al.getGroups() != null
+ && al.getGroups().size() > 0)
+ {
+ // pre 2.8.1 behaviour
+ // check to see if we should transfer annotation colours
+ propagateAnnColour = true;
+ for (jalview.datamodel.SequenceGroup sg : al.getGroups())
+ {
+ if (sg.cs instanceof AnnotationColourGradient)
+ {
+ propagateAnnColour = false;
+ }
+ }
+ }
+ // int find annotation
+ if (annAlignment.getAlignmentAnnotation() != null)
+ {
+ for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
+ {
+ if (annAlignment.getAlignmentAnnotation()[i].label
+ .equals(viewAnnColour.getAnnotation()))
+ {
+ if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
+ {
+ annAlignment.getAlignmentAnnotation()[i]
+ .setThreshold(new jalview.datamodel.GraphLine(
+ viewAnnColour.getThreshold(), "Threshold",
+ java.awt.Color.black)
+
+ );
+ }
+
+ if (viewAnnColour.getColourScheme().equals("None"))
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ new java.awt.Color(viewAnnColour.getMinColour()),
+ new java.awt.Color(viewAnnColour.getMaxColour()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ GetUserColourScheme(jms,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ ColourSchemeProperty.getColour(al,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ if (viewAnnColour.hasPerSequence())
+ {
+ ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
+ .isPerSequence());
+ }
+ if (viewAnnColour.hasPredefinedColours())
+ {
+ ((AnnotationColourGradient) cs)
+ .setPredefinedColours(viewAnnColour
+ .isPredefinedColours());
+ }
+ if (propagateAnnColour && al.getGroups() != null)
+ {
+ // Also use these settings for all the groups
+ for (int g = 0; g < al.getGroups().size(); g++)
+ {
+ jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
+
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ /*
+ * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
+ * new AnnotationColourGradient(
+ * annAlignment.getAlignmentAnnotation()[i], new
+ * java.awt.Color(viewAnnColour. getMinColour()), new
+ * java.awt.Color(viewAnnColour. getMaxColour()),
+ * viewAnnColour.getAboveThreshold()); } else
+ */
+ {
+ sg.cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i], sg.cs,
+ viewAnnColour.getAboveThreshold());
+ if (cs instanceof AnnotationColourGradient)
+ {
+ if (viewAnnColour.hasPerSequence())
+ {
+ ((AnnotationColourGradient) cs)
+ .setSeqAssociated(viewAnnColour.isPerSequence());
+ }
+ if (viewAnnColour.hasPredefinedColours())
+ {
+ ((AnnotationColourGradient) cs)
+ .setPredefinedColours(viewAnnColour
+ .isPredefinedColours());
+ }
+ }
+ }
+
+ }
+ }
+
+ break;
+ }
+
+ }
+ }
+ return cs;
+ }
+
private void reorderAutoannotation(AlignFrame af, Alignment al,
ArrayList autoAlan)
{
@@ -3847,14 +3971,18 @@ public class Jalview2XML
{ // make this dataset sequence sq's dataset sequence
sq.setDatasetSequence(dsq);
// and update the current dataset alignment
- if (ds==null) {
- if (dseqs!=null) {
+ if (ds == null)
+ {
+ if (dseqs != null)
+ {
if (!dseqs.contains(dsq))
{
dseqs.add(dsq);
}
- } else {
- if (ds.findIndex(dsq)<0)
+ }
+ else
+ {
+ if (ds.findIndex(dsq) < 0)
{
ds.addSequence(dsq);
}
@@ -3890,7 +4018,8 @@ public class Jalview2XML
}
// TODO: merges will never happen if we 'know' we have the real dataset
// sequence - this should be detected when id==dssid
- System.err.println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
+ System.err
+ .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
// + (pre ? "prepended" : "") + " "
// + (post ? "appended" : ""));
}