X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=7a71d79f04b99c17aee36a72d750173198786767;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=14650a9d5d102a637091312b238822c6b43d4c2d;hpb=e826112670b160df06adb4030835624248ac4a8a;p=jalview.git
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 14650a9..7a71d79 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,19 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * 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
+ * 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.
- *
- * 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
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -38,14 +39,21 @@ import jalview.schemabinding.version2.*;
import jalview.schemes.*;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.dm.AAConSettings;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.AutoCalcSetting;
+import jalview.ws.params.WsParamSetI;
/**
* Write out the current jalview desktop state as a Jalview XML stream.
- *
+ *
* Note: the vamsas objects referred to here are primitive versions of the
* VAMSAS project schema elements - they are not the same and most likely never
* will be :)
- *
+ *
* @author $author$
* @version $Revision: 1.134 $
*/
@@ -53,7 +61,7 @@ public class Jalview2XML
{
/**
* create/return unique hash string for sq
- *
+ *
* @param sq
* @return new or existing unique string for sq
*/
@@ -259,7 +267,7 @@ public class Jalview2XML
/**
* Writes a jalview project archive to the given Jar output stream.
- *
+ *
* @param jout
*/
public void SaveState(JarOutputStream jout)
@@ -271,6 +279,8 @@ public class Jalview2XML
return;
}
+ Hashtable dsses = new Hashtable();
+
try
{
@@ -325,6 +335,7 @@ public class Jalview2XML
}
int ap, apSize = af.alignPanels.size();
+
for (ap = 0; ap < apSize; ap++)
{
AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
@@ -336,9 +347,21 @@ public class Jalview2XML
}
SaveState(apanel, fileName, jout);
+
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
+ if (!dsses.containsKey(dssid))
+ {
+ dsses.put(dssid, af);
+ }
+
}
}
}
+
+ writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
+ jout);
+
try
{
jout.flush();
@@ -368,6 +391,7 @@ public class Jalview2XML
int ap, apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
+ Hashtable dsses = new Hashtable();
for (ap = 0; ap < apSize; ap++)
{
AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
@@ -378,8 +402,14 @@ public class Jalview2XML
jfileName = jfileName + ".xml";
}
SaveState(apanel, jfileName, jout);
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
+ if (!dsses.containsKey(dssid))
+ {
+ dsses.put(dssid, af);
+ }
}
-
+ writeDatasetFor(dsses, fileName, jout);
try
{
jout.flush();
@@ -397,10 +427,26 @@ public class Jalview2XML
}
}
+ private void writeDatasetFor(Hashtable dsses,
+ String fileName, JarOutputStream jout)
+ {
+
+ for (String dssids : dsses.keySet())
+ {
+ AlignFrame _af = dsses.get(dssids);
+ String jfileName = fileName + " Dataset for " + _af.getTitle();
+ if (!jfileName.endsWith(".xml"))
+ {
+ jfileName = jfileName + ".xml";
+ }
+ SaveState(_af.alignPanel, jfileName, true, jout);
+ }
+ }
+
/**
* create a JalviewModel from an algnment view and marshall it to a
* JarOutputStream
- *
+ *
* @param ap
* panel to create jalview model for
* @param fileName
@@ -413,6 +459,28 @@ public class Jalview2XML
public JalviewModel SaveState(AlignmentPanel ap, String fileName,
JarOutputStream 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)
+ {
initSeqRefs();
Vector jmolViewIds = new Vector(); //
Vector userColours = new Vector();
@@ -423,7 +491,8 @@ public class Jalview2XML
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
+ object.setVersion(jalview.bin.Cache.getDefault("VERSION",
+ "Development Build"));
jalview.datamodel.AlignmentI jal = av.getAlignment();
@@ -442,6 +511,11 @@ public class Jalview2XML
{
// dataset id is the dataset's hashcode
vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
+ if (storeDS)
+ {
+ // switch jal and the dataset
+ jal = jal.getDataset();
+ }
}
if (jal.getProperties() != null)
{
@@ -457,13 +531,16 @@ public class Jalview2XML
}
JSeq jseq;
+ Set calcIdSet = new HashSet();
// SAVE SEQUENCES
String id = "";
- jalview.datamodel.SequenceI jds;
+ jalview.datamodel.SequenceI jds, jdatasq;
for (int i = 0; i < jal.getHeight(); i++)
{
jds = jal.getSequenceAt(i);
+ jdatasq = jds.getDatasetSequence() == null ? jds : jds
+ .getDatasetSequence();
id = seqHash(jds);
if (seqRefIds.get(id) != null)
@@ -495,28 +572,34 @@ public class Jalview2XML
jseq.setColour(av.getSequenceColour(jds).getRGB());
jseq.setId(id); // jseq id should be a string not a number
-
- if (av.hasHiddenRows())
+ if (!storeDS)
{
- jseq.setHidden(av.getAlignment().getHiddenSequences().isHidden(jds));
-
- if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
+ // Store any sequences this sequence represents
+ if (av.hasHiddenRows())
{
- jalview.datamodel.SequenceI[] reps = av.getRepresentedSequences(jal.getSequenceAt(i)).getSequencesInOrder(jal);
+ jseq.setHidden(av.getAlignment().getHiddenSequences()
+ .isHidden(jds));
- for (int h = 0; h < reps.length; h++)
+ if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
{
- if (reps[h] != jal.getSequenceAt(i))
+ jalview.datamodel.SequenceI[] reps = av
+ .getRepresentedSequences(jal.getSequenceAt(i))
+ .getSequencesInOrder(jal);
+
+ for (int h = 0; h < reps.length; h++)
{
- jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ if (reps[h] != jal.getSequenceAt(i))
+ {
+ jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ }
}
}
}
}
- if (jds.getDatasetSequence().getSequenceFeatures() != null)
+ if (jdatasq.getSequenceFeatures() != null)
{
- jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
+ jalview.datamodel.SequenceFeature[] sf = jdatasq
.getSequenceFeatures();
int index = 0;
while (index < sf.length)
@@ -558,9 +641,9 @@ public class Jalview2XML
}
}
- if (jds.getDatasetSequence().getPDBId() != null)
+ if (jdatasq.getPDBId() != null)
{
- Enumeration en = jds.getDatasetSequence().getPDBId().elements();
+ Enumeration en = jdatasq.getPDBId().elements();
while (en.hasMoreElements())
{
Pdbids pdb = new Pdbids();
@@ -569,7 +652,10 @@ public class Jalview2XML
pdb.setId(entry.getId());
pdb.setType(entry.getType());
-
+ //
+ // store any JMol views associated with this seqeunce
+ // this section copes with duplicate entries in the project, so a
+ // dataset only view *should* be coped with sensibly
AppJmol jmol;
// This must have been loaded, is it still visible?
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -609,8 +695,8 @@ public class Jalview2XML
for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++)
{
-// if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
- if (jds==jmol.jmb.sequence[peid][smap])
+ // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+ if (jds == jmol.jmb.sequence[peid][smap])
{
StructureState state = new StructureState();
state.setVisible(true);
@@ -636,6 +722,7 @@ public class Jalview2XML
}
pdb.addStructureState(state);
}
+
}
}
}
@@ -704,7 +791,7 @@ public class Jalview2XML
jms.addJSeq(jseq);
}
- if (av.hasHiddenRows())
+ if (!storeDS && av.hasHiddenRows())
{
jal = av.getAlignment();
}
@@ -748,7 +835,7 @@ public class Jalview2XML
// SAVE TREES
// /////////////////////////////////
- if (av.currentTree != null)
+ if (!storeDS && av.currentTree != null)
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
@@ -790,142 +877,33 @@ public class Jalview2XML
}
}
}
-
// SAVE ANNOTATIONS
/**
* store forward refs from an annotationRow to any groups
*/
IdentityHashMap groupRefs = new IdentityHashMap();
- if (jal.getAlignmentAnnotation() != null)
+ if (storeDS)
{
- jalview.datamodel.AlignmentAnnotation[] aa = jal
- .getAlignmentAnnotation();
-
- for (int i = 0; i < aa.length; i++)
+ for (SequenceI sq : jal.getSequences())
{
- Annotation an = new Annotation();
-
- if (aa[i].annotationId != null)
- {
- annotationIds.put(aa[i].annotationId, aa[i]);
- }
-
- an.setId(aa[i].annotationId);
-
- an.setVisible(aa[i].visible);
-
- an.setDescription(aa[i].description);
-
- if (aa[i].sequenceRef != null)
- {
- // TODO later annotation sequenceRef should be the XML ID of the
- // sequence rather than its display name
- an.setSequenceRef(aa[i].sequenceRef.getName());
- }
- if (aa[i].groupRef != null)
- {
- Object groupIdr = groupRefs.get(aa[i].groupRef);
- if (groupIdr == null)
- {
- // make a locally unique String
- groupRefs.put(aa[i].groupRef,
- groupIdr = ("" + System.currentTimeMillis()
- + aa[i].groupRef.getName() + groupRefs.size()));
- }
- an.setGroupRef(groupIdr.toString());
- }
-
- // store all visualization attributes for annotation
- an.setGraphHeight(aa[i].graphHeight);
- an.setCentreColLabels(aa[i].centreColLabels);
- an.setScaleColLabels(aa[i].scaleColLabel);
- an.setShowAllColLabels(aa[i].showAllColLabels);
- an.setBelowAlignment(aa[i].belowAlignment);
-
- if (aa[i].graph > 0)
- {
- an.setGraph(true);
- an.setGraphType(aa[i].graph);
- an.setGraphGroup(aa[i].graphGroup);
- if (aa[i].getThreshold() != null)
- {
- ThresholdLine line = new ThresholdLine();
- line.setLabel(aa[i].getThreshold().label);
- line.setValue(aa[i].getThreshold().value);
- line.setColour(aa[i].getThreshold().colour.getRGB());
- an.setThresholdLine(line);
- }
- }
- else
- {
- an.setGraph(false);
- }
-
- an.setLabel(aa[i].label);
-
- if (aa[i] == av.getAlignmentQualityAnnot() || aa[i] == av.getAlignmentConservationAnnotation()
- || aa[i] == av.getAlignmentConsensusAnnotation() || aa[i].autoCalculated)
- {
- // new way of indicating autocalculated annotation -
- an.setAutoCalculated(aa[i].autoCalculated);
- }
- if (aa[i].hasScore())
+ // Store annotation on dataset sequences only
+ jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation();
+ if (aa != null && aa.length > 0)
{
- an.setScore(aa[i].getScore());
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
}
-
- if (aa[i].getCalcId()!=null)
- {
- an.setCalcId(aa[i].getCalcId());
- }
-
- AnnotationElement ae;
- if (aa[i].annotations != null)
- {
- an.setScoreOnly(false);
- for (int a = 0; a < aa[i].annotations.length; a++)
- {
- if ((aa[i] == null) || (aa[i].annotations[a] == null))
- {
- continue;
- }
-
- ae = new AnnotationElement();
- if (aa[i].annotations[a].description != null)
- ae.setDescription(aa[i].annotations[a].description);
- if (aa[i].annotations[a].displayCharacter != null)
- ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
-
- if (!Float.isNaN(aa[i].annotations[a].value))
- ae.setValue(aa[i].annotations[a].value);
-
- ae.setPosition(a);
- if (aa[i].annotations[a].secondaryStructure != ' '
- && aa[i].annotations[a].secondaryStructure != '\0')
- ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
- + "");
-
- if (aa[i].annotations[a].colour != null
- && aa[i].annotations[a].colour != java.awt.Color.black)
- {
- ae.setColour(aa[i].annotations[a].colour.getRGB());
- }
-
- an.addAnnotationElement(ae);
- if (aa[i].autoCalculated)
- {
- // only write one non-null entry into the annotation row -
- // sufficient to get the visualization attributes necessary to
- // display data
- continue;
- }
- }
- }
- else
- {
- an.setScoreOnly(true);
- }
- vamsasSet.addAnnotation(an);
+ }
+ }
+ else
+ {
+ if (jal.getAlignmentAnnotation() != null)
+ {
+ // Store the annotation shown on the alignment.
+ jalview.datamodel.AlignmentAnnotation[] aa = jal
+ .getAlignmentAnnotation();
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
}
}
// SAVE GROUPS
@@ -933,7 +911,7 @@ public class Jalview2XML
{
JGroup[] groups = new JGroup[jal.getGroups().size()];
int i = -1;
- for (jalview.datamodel.SequenceGroup sg:jal.getGroups())
+ for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
{
groups[++i] = new JGroup();
@@ -964,10 +942,10 @@ 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)
{
@@ -993,6 +971,7 @@ public class Jalview2XML
groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
+ groups[i].setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
for (int s = 0; s < sg.getSize(); s++)
{
jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
@@ -1003,234 +982,238 @@ public class Jalview2XML
jms.setJGroup(groups);
}
+ if (!storeDS)
+ {
+ // /////////SAVE VIEWPORT
+ Viewport view = new Viewport();
+ view.setTitle(ap.alignFrame.getTitle());
+ view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
+ av.getSequenceSetId()));
+ view.setId(av.getViewId());
+ view.setViewName(av.viewName);
+ view.setGatheredViews(av.gatherViewsHere);
+
+ if (ap.av.explodedPosition != null)
+ {
+ view.setXpos(av.explodedPosition.x);
+ view.setYpos(av.explodedPosition.y);
+ view.setWidth(av.explodedPosition.width);
+ view.setHeight(av.explodedPosition.height);
+ }
+ else
+ {
+ view.setXpos(ap.alignFrame.getBounds().x);
+ view.setYpos(ap.alignFrame.getBounds().y);
+ view.setWidth(ap.alignFrame.getBounds().width);
+ view.setHeight(ap.alignFrame.getBounds().height);
+ }
- // /////////SAVE VIEWPORT
- Viewport view = new Viewport();
- view.setTitle(ap.alignFrame.getTitle());
- view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
- av.getSequenceSetId()));
- view.setId(av.getViewId());
- view.setViewName(av.viewName);
- view.setGatheredViews(av.gatherViewsHere);
-
- if (ap.av.explodedPosition != null)
- {
- view.setXpos(av.explodedPosition.x);
- view.setYpos(av.explodedPosition.y);
- view.setWidth(av.explodedPosition.width);
- view.setHeight(av.explodedPosition.height);
- }
- else
- {
- view.setXpos(ap.alignFrame.getBounds().x);
- view.setYpos(ap.alignFrame.getBounds().y);
- view.setWidth(ap.alignFrame.getBounds().width);
- view.setHeight(ap.alignFrame.getBounds().height);
- }
-
- view.setStartRes(av.startRes);
- view.setStartSeq(av.startSeq);
-
- if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
- {
- view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
- userColours, jms));
- }
- else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
- {
- jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
- .getGlobalColourScheme();
+ view.setStartRes(av.startRes);
+ view.setStartSeq(av.startSeq);
- AnnotationColours ac = new AnnotationColours();
- ac.setAboveThreshold(acg.getAboveThreshold());
- ac.setThreshold(acg.getAnnotationThreshold());
- ac.setAnnotation(acg.getAnnotation());
- if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
- ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+ view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
userColours, jms));
}
+ else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
+ {
+ AnnotationColours ac = constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) av
+ .getGlobalColourScheme(),
+ userColours, jms);
+
+ view.setAnnotationColours(ac);
+ view.setBgColour("AnnotationColourGradient");
+ }
else
{
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg
- .getBaseColour()));
+ view.setBgColour(ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
}
- ac.setMaxColour(acg.getMaxColour().getRGB());
- ac.setMinColour(acg.getMinColour().getRGB());
- view.setAnnotationColours(ac);
- view.setBgColour("AnnotationColourGradient");
- }
- else
- {
- view.setBgColour(ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
- }
-
- ColourSchemeI cs = av.getGlobalColourScheme();
+ ColourSchemeI cs = av.getGlobalColourScheme();
- if (cs != null)
- {
- if (cs.conservationApplied())
+ if (cs != null)
{
- view.setConsThreshold(cs.getConservationInc());
- if (cs instanceof jalview.schemes.UserColourScheme)
+ if (cs.conservationApplied())
{
- view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+ view.setConsThreshold(cs.getConservationInc());
+ if (cs instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+ }
}
- }
- if (cs instanceof ResidueColourScheme)
- {
- view.setPidThreshold(cs.getThreshold());
+ if (cs instanceof ResidueColourScheme)
+ {
+ view.setPidThreshold(cs.getThreshold());
+ }
}
- }
- view.setConservationSelected(av.getConservationSelected());
- view.setPidSelected(av.getAbovePIDThreshold());
- view.setFontName(av.font.getName());
- view.setFontSize(av.font.getSize());
- view.setFontStyle(av.font.getStyle());
- view.setRenderGaps(av.renderGaps);
- view.setShowAnnotation(av.getShowAnnotation());
- view.setShowBoxes(av.getShowBoxes());
- view.setShowColourText(av.getColourText());
- view.setShowFullId(av.getShowJVSuffix());
- view.setRightAlignIds(av.rightAlignIds);
- view.setShowSequenceFeatures(av.showSequenceFeatures);
- view.setShowText(av.getShowText());
- view.setShowUnconserved(av.getShowUnconserved());
- view.setWrapAlignment(av.getWrapAlignment());
- view.setTextCol1(av.textColour.getRGB());
- view.setTextCol2(av.textColour2.getRGB());
- view.setTextColThreshold(av.thresholdTextColour);
- view.setShowConsensusHistogram(av.isShowConsensusHistogram());
- view.setShowSequenceLogo(av.isShowSequenceLogo());
- view.setShowGroupConsensus(av.isShowGroupConsensus());
- view.setShowGroupConservation(av.isShowGroupConservation());
- view.setShowNPfeatureTooltip(av.isShowNpFeats());
- view.setShowDbRefTooltip(av.isShowDbRefs());
- view.setFollowHighlight(av.followHighlight);
- view.setFollowSelection(av.followSelection);
- view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
- if (av.featuresDisplayed != null)
- {
- jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
+ view.setConservationSelected(av.getConservationSelected());
+ view.setPidSelected(av.getAbovePIDThreshold());
+ view.setFontName(av.font.getName());
+ view.setFontSize(av.font.getSize());
+ view.setFontStyle(av.font.getStyle());
+ view.setRenderGaps(av.renderGaps);
+ view.setShowAnnotation(av.getShowAnnotation());
+ view.setShowBoxes(av.getShowBoxes());
+ view.setShowColourText(av.getColourText());
+ view.setShowFullId(av.getShowJVSuffix());
+ view.setRightAlignIds(av.rightAlignIds);
+ view.setShowSequenceFeatures(av.showSequenceFeatures);
+ view.setShowText(av.getShowText());
+ view.setShowUnconserved(av.getShowUnconserved());
+ view.setWrapAlignment(av.getWrapAlignment());
+ view.setTextCol1(av.textColour.getRGB());
+ view.setTextCol2(av.textColour2.getRGB());
+ view.setTextColThreshold(av.thresholdTextColour);
+ view.setShowConsensusHistogram(av.isShowConsensusHistogram());
+ view.setShowSequenceLogo(av.isShowSequenceLogo());
+ view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
+ view.setShowGroupConsensus(av.isShowGroupConsensus());
+ view.setShowGroupConservation(av.isShowGroupConservation());
+ view.setShowNPfeatureTooltip(av.isShowNpFeats());
+ view.setShowDbRefTooltip(av.isShowDbRefs());
+ view.setFollowHighlight(av.followHighlight);
+ view.setFollowSelection(av.followSelection);
+ view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
+ if (av.featuresDisplayed != null)
+ {
+ jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+ String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
- Vector settingsAdded = new Vector();
- Object gstyle = null;
- GraduatedColor gcol = null;
- if (renderOrder != null)
- {
- for (int ro = 0; ro < renderOrder.length; ro++)
+ Vector settingsAdded = new Vector();
+ Object gstyle = null;
+ GraduatedColor gcol = null;
+ if (renderOrder != null)
{
- gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getFeatureStyle(renderOrder[ro]);
- Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
- if (gstyle instanceof GraduatedColor)
- {
- gcol = (GraduatedColor) gstyle;
- setting.setColour(gcol.getMaxColor().getRGB());
- setting.setMincolour(gcol.getMinColor().getRGB());
- setting.setMin(gcol.getMin());
- setting.setMax(gcol.getMax());
- setting.setColourByLabel(gcol.isColourByLabel());
- setting.setAutoScale(gcol.isAutoScale());
- setting.setThreshold(gcol.getThresh());
- setting.setThreshstate(gcol.getThreshType());
+ for (int ro = 0; ro < renderOrder.length; ro++)
+ {
+ gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getFeatureStyle(renderOrder[ro]);
+ Setting setting = new Setting();
+ setting.setType(renderOrder[ro]);
+ if (gstyle instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) gstyle;
+ setting.setColour(gcol.getMaxColor().getRGB());
+ setting.setMincolour(gcol.getMinColor().getRGB());
+ setting.setMin(gcol.getMin());
+ setting.setMax(gcol.getMax());
+ setting.setColourByLabel(gcol.isColourByLabel());
+ setting.setAutoScale(gcol.isAutoScale());
+ setting.setThreshold(gcol.getThresh());
+ setting.setThreshstate(gcol.getThreshType());
+ }
+ else
+ {
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(renderOrder[ro]).getRGB());
+ }
+
+ setting.setDisplay(av.featuresDisplayed
+ .containsKey(renderOrder[ro]));
+ float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getOrder(renderOrder[ro]);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(renderOrder[ro]);
}
- else
+ }
+
+ // Make sure we save none displayed feature settings
+ Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+ .keySet().iterator();
+ while (en.hasNext())
+ {
+ String key = en.next().toString();
+ if (settingsAdded.contains(key))
{
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getColour(renderOrder[ro]).getRGB());
+ continue;
}
- setting.setDisplay(av.featuresDisplayed
- .containsKey(renderOrder[ro]));
+ Setting setting = new Setting();
+ setting.setType(key);
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(key).getRGB());
+
+ setting.setDisplay(false);
float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getOrder(renderOrder[ro]);
+ .getOrder(key);
if (rorder > -1)
{
setting.setOrder(rorder);
}
fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
+ settingsAdded.addElement(key);
}
- }
-
- // Make sure we save none displayed feature settings
- Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
- .keys();
- while (en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- if (settingsAdded.contains(key))
+ en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+ .keySet().iterator();
+ Vector groupsAdded = new Vector();
+ while (en.hasNext())
{
- continue;
+ String grp = en.next().toString();
+ if (groupsAdded.contains(grp))
+ {
+ continue;
+ }
+ Group g = new Group();
+ g.setName(grp);
+ g.setDisplay(((Boolean) ap.seqPanel.seqCanvas
+ .getFeatureRenderer().featureGroups.get(grp))
+ .booleanValue());
+ fs.addGroup(g);
+ groupsAdded.addElement(grp);
}
+ jms.setFeatureSettings(fs);
- Setting setting = new Setting();
- setting.setType(key);
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getColour(key).getRGB());
+ }
- setting.setDisplay(false);
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
- key);
- if (rorder > -1)
+ if (av.hasHiddenColumns())
+ {
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().getHiddenColumns() == null)
{
- setting.setOrder(rorder);
+ warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
}
- fs.addSetting(setting);
- settingsAdded.addElement(key);
- }
- en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
- Vector groupsAdded = new Vector();
- while (en.hasMoreElements())
- {
- String grp = en.nextElement().toString();
- if (groupsAdded.contains(grp))
+ else
{
- continue;
+ for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
+ .size(); c++)
+ {
+ int[] region = (int[]) av.getColumnSelection()
+ .getHiddenColumns().elementAt(c);
+ HiddenColumns hc = new HiddenColumns();
+ hc.setStart(region[0]);
+ hc.setEnd(region[1]);
+ view.addHiddenColumns(hc);
+ }
}
- Group g = new Group();
- g.setName(grp);
- g.setDisplay(((Boolean) ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
- .get(grp)).booleanValue());
- fs.addGroup(g);
- groupsAdded.addElement(grp);
}
- jms.setFeatureSettings(fs);
-
- }
-
- if (av.hasHiddenColumns())
- {
- if (av.getColumnSelection() == null
- || av.getColumnSelection().getHiddenColumns() == null)
- {
- warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
- }
- else
+ if (calcIdSet.size() > 0)
{
- for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
- .size(); c++)
+ for (String calcId : calcIdSet)
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(c);
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- view.addHiddenColumns(hc);
+ if (calcId.trim().length() > 0)
+ {
+ CalcIdParam cidp = createCalcIdParam(calcId, av);
+ // Some calcIds have no parameters.
+ if (cidp != null)
+ {
+ view.addCalcIdParam(cidp);
+ }
+ }
}
}
- }
-
- jms.addViewport(view);
+ jms.addViewport(view);
+ }
object.setJalviewModelSequence(jms);
object.getVamsasModel().addSequenceSet(vamsasSet);
@@ -1259,6 +1242,267 @@ public class Jalview2XML
return object;
}
+ 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++)
+ {
+ Annotation an = new Annotation();
+
+ if (aa[i].annotationId != null)
+ {
+ annotationIds.put(aa[i].annotationId, aa[i]);
+ }
+
+ an.setId(aa[i].annotationId);
+
+ an.setVisible(aa[i].visible);
+
+ an.setDescription(aa[i].description);
+
+ if (aa[i].sequenceRef != null)
+ {
+ // TODO later annotation sequenceRef should be the XML ID of the
+ // sequence rather than its display name
+ an.setSequenceRef(aa[i].sequenceRef.getName());
+ }
+ if (aa[i].groupRef != null)
+ {
+ Object groupIdr = groupRefs.get(aa[i].groupRef);
+ if (groupIdr == null)
+ {
+ // make a locally unique String
+ groupRefs.put(aa[i].groupRef,
+ groupIdr = ("" + System.currentTimeMillis()
+ + aa[i].groupRef.getName() + groupRefs.size()));
+ }
+ an.setGroupRef(groupIdr.toString());
+ }
+
+ // store all visualization attributes for annotation
+ an.setGraphHeight(aa[i].graphHeight);
+ an.setCentreColLabels(aa[i].centreColLabels);
+ an.setScaleColLabels(aa[i].scaleColLabel);
+ an.setShowAllColLabels(aa[i].showAllColLabels);
+ an.setBelowAlignment(aa[i].belowAlignment);
+
+ if (aa[i].graph > 0)
+ {
+ an.setGraph(true);
+ an.setGraphType(aa[i].graph);
+ an.setGraphGroup(aa[i].graphGroup);
+ if (aa[i].getThreshold() != null)
+ {
+ ThresholdLine line = new ThresholdLine();
+ line.setLabel(aa[i].getThreshold().label);
+ line.setValue(aa[i].getThreshold().value);
+ line.setColour(aa[i].getThreshold().colour.getRGB());
+ an.setThresholdLine(line);
+ }
+ }
+ else
+ {
+ an.setGraph(false);
+ }
+
+ an.setLabel(aa[i].label);
+
+ if (aa[i] == av.getAlignmentQualityAnnot()
+ || aa[i] == av.getAlignmentConservationAnnotation()
+ || aa[i] == av.getAlignmentConsensusAnnotation()
+ || aa[i].autoCalculated)
+ {
+ // new way of indicating autocalculated annotation -
+ an.setAutoCalculated(aa[i].autoCalculated);
+ }
+ if (aa[i].hasScore())
+ {
+ an.setScore(aa[i].getScore());
+ }
+
+ if (aa[i].getCalcId() != null)
+ {
+ calcIdSet.add(aa[i].getCalcId());
+ an.setCalcId(aa[i].getCalcId());
+ }
+
+ AnnotationElement ae;
+ if (aa[i].annotations != null)
+ {
+ an.setScoreOnly(false);
+ for (int a = 0; a < aa[i].annotations.length; a++)
+ {
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))
+ {
+ continue;
+ }
+
+ ae = new AnnotationElement();
+ if (aa[i].annotations[a].description != null)
+ ae.setDescription(aa[i].annotations[a].description);
+ if (aa[i].annotations[a].displayCharacter != null)
+ ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+
+ if (!Float.isNaN(aa[i].annotations[a].value))
+ ae.setValue(aa[i].annotations[a].value);
+
+ ae.setPosition(a);
+ if (aa[i].annotations[a].secondaryStructure != ' '
+ && aa[i].annotations[a].secondaryStructure != '\0')
+ ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ + "");
+
+ if (aa[i].annotations[a].colour != null
+ && aa[i].annotations[a].colour != java.awt.Color.black)
+ {
+ ae.setColour(aa[i].annotations[a].colour.getRGB());
+ }
+
+ an.addAnnotationElement(ae);
+ if (aa[i].autoCalculated)
+ {
+ // only write one non-null entry into the annotation row -
+ // sufficient to get the visualization attributes necessary to
+ // display data
+ continue;
+ }
+ }
+ }
+ else
+ {
+ an.setScoreOnly(true);
+ }
+ if (!storeDS || (storeDS && !aa[i].autoCalculated))
+ {
+ // skip autocalculated annotation - these are only provided for
+ // alignments
+ vamsasSet.addAnnotation(an);
+ }
+ }
+
+ }
+
+ private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
+ {
+ AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
+ if (settings != null)
+ {
+ CalcIdParam vCalcIdParam = new CalcIdParam();
+ vCalcIdParam.setCalcId(calcId);
+ vCalcIdParam.addServiceURL(settings.getServiceURI());
+ // generic URI allowing a third party to resolve another instance of the
+ // service used for this calculation
+ for (String urls : settings.getServiceURLs())
+ {
+ vCalcIdParam.addServiceURL(urls);
+ }
+ vCalcIdParam.setVersion("1.0");
+ if (settings.getPreset() != null)
+ {
+ WsParamSetI setting = settings.getPreset();
+ vCalcIdParam.setName(setting.getName());
+ vCalcIdParam.setDescription(setting.getDescription());
+ }
+ else
+ {
+ vCalcIdParam.setName("");
+ vCalcIdParam.setDescription("Last used parameters");
+ }
+ // need to be able to recover 1) settings 2) user-defined presets or
+ // recreate settings from preset 3) predefined settings provided by
+ // service - or settings that can be transferred (or discarded)
+ vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n",
+ "|\\n|"));
+ vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
+ // todo - decide if updateImmediately is needed for any projects.
+
+ return vCalcIdParam;
+ }
+ return null;
+ }
+
+ private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
+ AlignViewport av)
+ {
+ if (calcIdParam.getVersion().equals("1.0"))
+ {
+ Jws2Instance service = Jws2Discoverer.getDiscoverer()
+ .getPreferredServiceFor(calcIdParam.getServiceURL());
+ if (service != null)
+ {
+ WsParamSetI parmSet = null;
+ try
+ {
+ parmSet = service.getParamStore().parseServiceParameterFile(
+ calcIdParam.getName(), calcIdParam.getDescription(),
+ calcIdParam.getServiceURL(),
+ calcIdParam.getParameters().replace("|\\n|", "\n"));
+ } catch (IOException x)
+ {
+ warn("Couldn't parse parameter data for "
+ + calcIdParam.getCalcId(), x);
+ return false;
+ }
+ List argList = null;
+ if (calcIdParam.getName().length() > 0)
+ {
+ parmSet = service.getParamStore()
+ .getPreset(calcIdParam.getName());
+ if (parmSet != null)
+ {
+ // TODO : check we have a good match with settings in AACon -
+ // otherwise we'll need to create a new preset
+ }
+ }
+ else
+ {
+ argList = parmSet.getArguments();
+ parmSet = null;
+ }
+ AAConSettings settings = new AAConSettings(
+ calcIdParam.isAutoUpdate(), service, parmSet, argList);
+ av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
+ calcIdParam.isNeedsUpdate());
+ return true;
+ }
+ else
+ {
+ warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ return false;
+ }
+ }
+ throw new Error("Unsupported Version for calcIdparam "
+ + calcIdParam.toString());
+ }
+
/**
* External mapping between jalview objects and objects yielding a valid and
* unique object ID string. This is null for normal Jalview project IO, but
@@ -1270,7 +1514,7 @@ public class Jalview2XML
/**
* Construct a unique ID for jvobj using either existing bindings or if none
* exist, the result of the hashcode call for the object.
- *
+ *
* @param jvobj
* jalview data object
* @return unique ID for referring to jvobj
@@ -1301,7 +1545,7 @@ public class Jalview2XML
/**
* return local jalview object mapped to ID, if it exists
- *
+ *
* @param idcode
* (may be null)
* @return null or object bound to idcode
@@ -1537,7 +1781,7 @@ public class Jalview2XML
/**
* Load a jalview project archive from a jar file
- *
+ *
* @param file
* - HTTP URL or filename
*/
@@ -1548,6 +1792,8 @@ public class Jalview2XML
try
{
+ // create list to store references for any new Jmol viewers created
+ newStructureViewers = new Vector();
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
@@ -1555,10 +1801,26 @@ public class Jalview2XML
jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
af = LoadJalviewAlign(jprovider);
+
} catch (MalformedURLException e)
{
errorMessage = "Invalid URL format for '" + file + "'";
reportErrors();
+ } finally
+ {
+ try
+ {
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+ public void run()
+ {
+ setLoadingFinishedForNewStructureViewers();
+ };
+ });
+ } catch (Exception x)
+ {
+
+ }
}
return af;
}
@@ -1607,7 +1869,7 @@ public class Jalview2XML
* initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
* themselves. Any null fields will be initialised with default values,
* non-null fields are left alone.
- *
+ *
* @param jprovider
* @return
*/
@@ -1631,7 +1893,7 @@ public class Jalview2XML
frefedSequence = new Vector();
}
- jalview.gui.AlignFrame af = null;
+ jalview.gui.AlignFrame af = null, _af = null;
Hashtable gatherToThisFrame = new Hashtable();
final String file = jprovider.getFilename();
try
@@ -1658,10 +1920,14 @@ public class Jalview2XML
object = (JalviewModel) unmar.unmarshal(in);
if (true) // !skipViewport(object))
{
- af = LoadFromObject(object, file, true, jprovider);
- if (af.viewport.gatherViewsHere)
+ _af = LoadFromObject(object, file, true, jprovider);
+ if (object.getJalviewModelSequence().getViewportCount() > 0)
{
- gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ af = _af;
+ if (af.viewport.gatherViewsHere)
+ {
+ gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ }
}
}
entryCount++;
@@ -1828,7 +2094,7 @@ public class Jalview2XML
}
;
out.close();
- String t=outFile.getAbsolutePath();
+ String t = outFile.getAbsolutePath();
alreadyLoadedPDB.put(pdbId, t);
return t;
}
@@ -1865,7 +2131,7 @@ public class Jalview2XML
/**
* Load alignment frame from jalview XML DOM object
- *
+ *
* @param object
* DOM
* @param file
@@ -1884,7 +2150,9 @@ public class Jalview2XML
JalviewModelSequence jms = object.getJalviewModelSequence();
- Viewport view = jms.getViewport(0);
+ Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
+ : null;
+
// ////////////////////////////////
// LOAD SEQUENCES
@@ -1926,8 +2194,7 @@ public class Jalview2XML
hiddenSeqs = new Vector();
}
- hiddenSeqs.addElement(seqRefIds
- .get(seqId));
+ hiddenSeqs.addElement(seqRefIds.get(seqId));
}
}
@@ -2148,16 +2415,19 @@ public class Jalview2XML
// Construct new annotation from model.
AnnotationElement[] ae = an[i].getAnnotationElement();
jalview.datamodel.Annotation[] anot = null;
-
+ java.awt.Color firstColour = null;
+ int anpos;
if (!an[i].getScoreOnly())
{
anot = new jalview.datamodel.Annotation[al.getWidth()];
for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
{
- if (ae[aa].getPosition() >= anot.length)
+ anpos = ae[aa].getPosition();
+
+ if (anpos >= anot.length)
continue;
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+ anot[anpos] = new jalview.datamodel.Annotation(
ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
(ae[aa].getSecondaryStructure() == null || ae[aa]
@@ -2173,8 +2443,11 @@ public class Jalview2XML
// {
// anot[ae[aa].getPosition()].displayCharacter = "";
// }
- anot[ae[aa].getPosition()].colour = new java.awt.Color(
- ae[aa].getColour());
+ anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
+ if (firstColour == null)
+ {
+ firstColour = anot[anpos].colour;
+ }
}
}
jalview.datamodel.AlignmentAnnotation jaa = null;
@@ -2190,7 +2463,7 @@ public class Jalview2XML
an[i].getGraphType());
jaa.graphGroup = an[i].getGraphGroup();
-
+ jaa._linecolour = firstColour;
if (an[i].getThresholdLine() != null)
{
jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
@@ -2210,25 +2483,22 @@ public class Jalview2XML
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot);
+ jaa._linecolour = firstColour;
}
- if (autoForView)
+ // register new annotation
+ if (an[i].getId() != null)
{
- // register new annotation
- if (an[i].getId() != null)
- {
- annotationIds.put(an[i].getId(), jaa);
- jaa.annotationId = an[i].getId();
- }
- // recover sequence association
- if (an[i].getSequenceRef() != null)
+ annotationIds.put(an[i].getId(), jaa);
+ jaa.annotationId = an[i].getId();
+ }
+ // recover sequence association
+ if (an[i].getSequenceRef() != null)
+ {
+ if (al.findName(an[i].getSequenceRef()) != null)
{
- if (al.findName(an[i].getSequenceRef()) != null)
- {
- jaa.createSequenceMapping(
- al.findName(an[i].getSequenceRef()), 1, true);
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(
- jaa);
- }
+ jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
+ 1, true);
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
}
}
// and make a note of any group association
@@ -2271,7 +2541,7 @@ public class Jalview2XML
}
if (an[i].hasBelowAlignment())
{
- jaa.belowAlignment=an[i].isBelowAlignment();
+ jaa.belowAlignment = an[i].isBelowAlignment();
}
jaa.setCalcId(an[i].getCalcId());
@@ -2288,14 +2558,13 @@ 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;
@@ -2306,6 +2575,12 @@ 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());
@@ -2357,6 +2632,10 @@ public class Jalview2XML
{
sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
}
+ if (groups[i].hasNormaliseSequenceLogo())
+ {
+ sg.setNormaliseSequenceLogo(groups[i].isNormaliseSequenceLogo());
+ }
if (groups[i].hasIgnoreGapsinConsensus())
{
sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
@@ -2400,10 +2679,19 @@ 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)
+ {
+ // only dataset in this model, so just return.
+ return null;
+ }
// ///////////////////////////////
// LOAD VIEWPORT
@@ -2447,6 +2735,13 @@ 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)
@@ -2638,13 +2933,12 @@ public class Jalview2XML
}
if (ids[p].getFile() != null)
{
- File mapkey=new File(ids[p].getFile());
+ File mapkey = new File(ids[p].getFile());
Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
.get(mapkey);
if (seqstrmaps == null)
{
- ((Hashtable) jmoldat[2]).put(
- mapkey,
+ ((Hashtable) jmoldat[2]).put(mapkey,
seqstrmaps = new Object[]
{ pdbFile, ids[p].getId(), new Vector(),
new Vector() });
@@ -2741,25 +3035,28 @@ public class Jalview2XML
{
newFileLoc = new StringBuffer();
}
- do {
+ do
+ {
// look for next filename in load statement
- newFileLoc.append(state.substring(cp,
- ncp = (state.indexOf("\"", ncp + 1) + 1)));
- String oldfilenam = state.substring(ncp,
- ecp = state.indexOf("\"", ncp));
- // recover the new mapping data for this old filename
- // have to normalize filename - since Jmol and jalview do filename
- // translation differently.
- Object[] filedat = oldFiles.get(new File(oldfilenam));
- newFileLoc.append(Platform.escapeString((String) filedat[0]));
- pdbfilenames.addElement((String) filedat[0]);
- pdbids.addElement((String) filedat[1]);
- seqmaps.addElement(((Vector) filedat[2])
- .toArray(new SequenceI[0]));
- newFileLoc.append("\"");
- cp = ecp + 1; // advance beyond last \" and set cursor so we can
- // look for next file statement.
- } while ((ncp=state.indexOf("/*file*/",cp))>-1);
+ newFileLoc.append(state.substring(cp,
+ ncp = (state.indexOf("\"", ncp + 1) + 1)));
+ String oldfilenam = state.substring(ncp,
+ ecp = state.indexOf("\"", ncp));
+ // recover the new mapping data for this old filename
+ // have to normalize filename - since Jmol and jalview do
+ // filename
+ // translation differently.
+ Object[] filedat = oldFiles.get(new File(oldfilenam));
+ newFileLoc.append(Platform
+ .escapeString((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement(((Vector) filedat[2])
+ .toArray(new SequenceI[0]));
+ newFileLoc.append("\"");
+ cp = ecp + 1; // advance beyond last \" and set cursor so we can
+ // look for next file statement.
+ } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
}
if (cp > 0)
{
@@ -2839,6 +3136,7 @@ public class Jalview2XML
sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
useinJmolsuperpos, usetoColourbyseq,
jmolColouring, fileloc, rect, vid);
+ addNewStructureViewer(sview);
} catch (OutOfMemoryError ex)
{
new OOMWarning("restoring structure view for PDB id "
@@ -2895,8 +3193,7 @@ public class Jalview2XML
}
if (usetoColourbyseq)
{
- comp.useAlignmentPanelForColourbyseq(ap,
- !jmolColouring);
+ comp.useAlignmentPanelForColourbyseq(ap, !jmolColouring);
}
else
{
@@ -2910,6 +3207,83 @@ public class Jalview2XML
return af;
}
+ /**
+ *
+ * @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)
+ {
+ sview.jmb.setFinishedLoadingFromArchive(false);
+ newStructureViewers.add(sview);
+ }
+ }
+
+ protected void setLoadingFinishedForNewStructureViewers()
+ {
+ if (newStructureViewers != null)
+ {
+ for (AppJmol sview : newStructureViewers)
+ {
+ sview.jmb.setFinishedLoadingFromArchive(true);
+ }
+ newStructureViewers.clear();
+ newStructureViewers = null;
+ }
+ }
+
AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
Alignment al, JalviewModelSequence jms, Viewport view,
String uniqueSeqSetId, String viewId,
@@ -2923,8 +3297,8 @@ public class Jalview2XML
for (int i = 0; i < JSEQ.length; i++)
{
- af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i),
- new java.awt.Color(JSEQ[i].getColour()));
+ af.viewport.setSequenceColour(af.viewport.getAlignment()
+ .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
}
af.viewport.gatherViewsHere = view.getGatheredViews();
@@ -3023,93 +3397,11 @@ 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());
- }
-
- // 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());
- }
-
- }
- }
-
- break;
- }
-
- }
- }
}
else
{
@@ -3145,8 +3437,8 @@ public class Jalview2XML
}
if (view.hasIgnoreGapsinConsensus())
{
- af.viewport.setIgnoreGapsConsensus(view
- .getIgnoreGapsinConsensus(), null);
+ af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
+ null);
}
if (view.hasFollowHighlight())
{
@@ -3173,6 +3465,10 @@ public class Jalview2XML
{
af.viewport.setShowSequenceLogo(false);
}
+ if (view.hasNormaliseSequenceLogo())
+ {
+ af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
+ }
if (view.hasShowDbRefTooltip())
{
af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
@@ -3272,16 +3568,158 @@ public class Jalview2XML
);
}
}
-
+ if (view.getCalcIdParam() != null)
+ {
+ for (CalcIdParam calcIdParam : view.getCalcIdParam())
+ {
+ if (calcIdParam != null)
+ {
+ if (recoverCalcIdParam(calcIdParam, af.viewport))
+ {
+ }
+ else
+ {
+ warn("Couldn't recover parameters for "
+ + calcIdParam.getCalcId());
+ }
+ }
+ }
+ }
af.setMenusFromViewport(af.viewport);
// TODO: we don't need to do this if the viewport is aready visible.
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
view.getHeight());
- af.alignPanel.updateAnnotation(false); // recompute any autoannotation
+ af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
reorderAutoannotation(af, al, autoAlan);
+ af.alignPanel.alignmentChanged();
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)
{
@@ -3302,21 +3740,34 @@ public class Jalview2XML
}
for (JvAnnotRow auan : autoAlan)
{
- visan.put(auan.template.label, auan);
+ visan.put(auan.template.label
+ + (auan.template.getCalcId() == null ? "" : "\t"
+ + auan.template.getCalcId()), auan);
}
int hSize = al.getAlignmentAnnotation().length;
ArrayList reorder = new ArrayList();
+ // work through any autoCalculated annotation already on the view
+ // removing it if it should be placed in a different location on the
+ // annotation panel.
+ List remains = new ArrayList(visan.keySet());
for (int h = 0; h < hSize; h++)
{
jalview.datamodel.AlignmentAnnotation jalan = al
.getAlignmentAnnotation()[h];
if (jalan.autoCalculated)
{
- JvAnnotRow valan = visan.get(jalan.label);
+ String k;
+ JvAnnotRow valan = visan.get(k = jalan.label);
+ if (jalan.getCalcId() != null)
+ {
+ valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
+ }
+
if (valan != null)
{
// delete the auto calculated row from the alignment
- al.deleteAnnotation(al.getAlignmentAnnotation()[h], false);
+ al.deleteAnnotation(jalan, false);
+ remains.remove(k);
hSize--;
h--;
if (valan != nullAnnot)
@@ -3338,6 +3789,18 @@ public class Jalview2XML
}
}
}
+ // Add any (possibly stale) autocalculated rows that were not appended to
+ // the view during construction
+ for (String other : remains)
+ {
+ JvAnnotRow othera = visan.get(other);
+ if (othera != nullAnnot && othera.template.getCalcId() != null
+ && othera.template.getCalcId().length() > 0)
+ {
+ reorder.add(othera);
+ }
+ }
+ // now put the automatic annotation in its correct place
int s = 0, srt[] = new int[reorder.size()];
JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
for (JvAnnotRow jvar : reorder)
@@ -3360,7 +3823,7 @@ public class Jalview2XML
/**
* TODO remove this method
- *
+ *
* @param view
* @return AlignFrame bound to sequenceSetId from view, if one exists. private
* AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
@@ -3371,7 +3834,7 @@ public class Jalview2XML
/**
* Check if the Jalview view contained in object should be skipped or not.
- *
+ *
* @param object
* @return true if view's sequenceSetId is a key in skipList
*/
@@ -3444,7 +3907,7 @@ public class Jalview2XML
}
/**
- *
+ *
* @param vamsasSeq
* sequence definition to create/merge dataset sequence for
* @param ds
@@ -3502,6 +3965,24 @@ public class Jalview2XML
if (sq != dsq)
{ // make this dataset sequence sq's dataset sequence
sq.setDatasetSequence(dsq);
+ // and update the current dataset alignment
+ if (ds == null)
+ {
+ if (dseqs != null)
+ {
+ if (!dseqs.contains(dsq))
+ {
+ dseqs.add(dsq);
+ }
+ }
+ else
+ {
+ if (ds.findIndex(dsq) < 0)
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ }
}
}
}
@@ -3528,11 +4009,12 @@ public class Jalview2XML
* sb.append(newres.substring(newres.length() - sq.getEnd() -
* dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
*/
- dsq.setSequence(sb.toString());
+ dsq.setSequence(newres);
}
// 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"); // ("
+ 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" : ""));
}
@@ -3568,7 +4050,7 @@ public class Jalview2XML
/**
* make a new dataset ID for this jalview dataset alignment
- *
+ *
* @param dataset
* @return
*/
@@ -3755,7 +4237,7 @@ public class Jalview2XML
/*
* (non-Javadoc)
- *
+ *
* @see java.lang.Object#finalize()
*/
@Override
@@ -3833,13 +4315,13 @@ public class Jalview2XML
* finalize and clearSeqRefs will not clear the tables when the Jalview2XML
* object goes out of scope. - also populates the datasetIds hashtable with
* alignment objects containing dataset sequences
- *
+ *
* @param vobj2jv
* Map from ID strings to jalview datamodel
* @param jv2vobj
* Map from jalview datamodel to ID strings
- *
- *
+ *
+ *
*/
public void setObjectMappingTables(Hashtable vobj2jv,
IdentityHashMap jv2vobj)
@@ -3911,7 +4393,7 @@ public class Jalview2XML
* set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
* objects created from the project archive. If string is null (default for
* construction) then suffix will be set automatically.
- *
+ *
* @param string
*/
public void setUniqueSetSuffix(String string)
@@ -3923,7 +4405,7 @@ public class Jalview2XML
/**
* uses skipList2 as the skipList for skipping views on sequence sets
* associated with keys in the skipList
- *
+ *
* @param skipList2
*/
public void setSkipList(Hashtable skipList2)