X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=3499f6d127a05d111f635dada32b152a157d4c8d;hb=18e6142e442c42442429c12ff48c7d637b855dca;hp=41dd71dcfe16126e760f780f3a8a7a1f26041793;hpb=18669497085ed86d73c77eb2f076943980bbc508;p=jalview.git
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 41dd71d..3499f6d 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
@@ -14,6 +14,7 @@
* 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;
@@ -38,7 +39,6 @@ import jalview.schemabinding.version2.*;
import jalview.schemes.*;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
-import jalview.ws.jws2.AAConClient;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -420,6 +420,26 @@ 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();
@@ -430,7 +450,7 @@ 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();
@@ -449,6 +469,11 @@ 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)
{
@@ -468,10 +493,11 @@ public class Jalview2XML
// 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)
@@ -503,29 +529,34 @@ 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)
@@ -567,9 +598,9 @@ 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();
@@ -578,7 +609,10 @@ 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();
@@ -645,6 +679,7 @@ public class Jalview2XML
}
pdb.addStructureState(state);
}
+
}
}
}
@@ -713,7 +748,7 @@ public class Jalview2XML
jms.addJSeq(jseq);
}
- if (av.hasHiddenRows())
+ if (!storeDS && av.hasHiddenRows())
{
jal = av.getAlignment();
}
@@ -757,7 +792,7 @@ 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
@@ -804,139 +839,26 @@ public class Jalview2XML
* 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++)
- {
- 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)
+ for (SequenceI sq:jal.getSequences())
{
- an.setGraph(true);
- an.setGraphType(aa[i].graph);
- an.setGraphGroup(aa[i].graphGroup);
- if (aa[i].getThreshold() != null)
+ // Store annotation on dataset sequences only
+ jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation();
+ if (aa!=null && aa.length>0)
{
- 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;
- }
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
}
}
- 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
@@ -1015,251 +937,255 @@ 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);
+ 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();
-
- 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)
+ {
+ jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
+ .getGlobalColourScheme();
+
+ 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");
+ }
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.setConsThreshold(cs.getConservationInc());
+ if (cs instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+ }
+ }
+
+ if (cs instanceof ResidueColourScheme)
{
- view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+ view.setPidThreshold(cs.getThreshold());
}
}
- if (cs instanceof ResidueColourScheme)
+ 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)
{
- view.setPidThreshold(cs.getThreshold());
- }
- }
+ 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;
-
- Vector settingsAdded = new Vector();
- Object gstyle = null;
- GraduatedColor gcol = null;
- if (renderOrder != null)
- {
- for (int ro = 0; ro < renderOrder.length; ro++)
+ String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+
+ 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)
+ for (int ro = 0; ro < renderOrder.length; ro++)
{
- 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());
+ 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
- Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
- .keySet().iterator();
- while (en.hasNext())
- {
- String key = en.next().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)
- {
- setting.setOrder(rorder);
- }
- fs.addSetting(setting);
- settingsAdded.addElement(key);
}
- en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
- .keySet().iterator();
- Vector groupsAdded = new Vector();
- while (en.hasNext())
+
+ if (av.hasHiddenColumns())
{
- String grp = en.next().toString();
- if (groupsAdded.contains(grp))
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().getHiddenColumns() == null)
{
- continue;
+ warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
}
- 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
- {
- for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
- .size(); c++)
+ else
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(c);
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- view.addHiddenColumns(hc);
+ 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);
+ }
}
}
- }
- if (calcIdSet.size() > 0)
- {
- for (String calcId : calcIdSet)
+ if (calcIdSet.size() > 0)
{
- if (calcId.trim().length() > 0)
+ for (String calcId : calcIdSet)
{
- CalcIdParam cidp = createCalcIdParam(calcId, av);
- // Some calcIds have no parameters.
- if (cidp != null)
+ if (calcId.trim().length() > 0)
{
- view.addCalcIdParam(cidp);
+ 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);
@@ -1288,6 +1214,145 @@ public class Jalview2XML
return object;
}
+ 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);
@@ -1679,12 +1744,27 @@ public class Jalview2XML
jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
af = LoadJalviewAlign(jprovider);
- setLoadingFinishedForNewStructureViewers();
+
} 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;
}
@@ -1756,7 +1836,7 @@ 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
@@ -1783,10 +1863,15 @@ 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 (object.getJalviewModelSequence().getViewportCount() > 1
+ && af.viewport.gatherViewsHere)
+ {
+ gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ }
}
}
entryCount++;
@@ -2009,7 +2094,8 @@ public class Jalview2XML
JalviewModelSequence jms = object.getJalviewModelSequence();
- Viewport view = jms.getViewport(0);
+ Viewport view = (jms.getViewportCount()>0) ? jms.getViewport(0) : null;
+
// ////////////////////////////////
// LOAD SEQUENCES
@@ -2534,7 +2620,11 @@ public class Jalview2XML
}
}
-
+ if (view==null)
+ {
+ // only dataset in this model, so just return.
+ return null;
+ }
// ///////////////////////////////
// LOAD VIEWPORT
@@ -3224,7 +3314,14 @@ public class Jalview2XML
.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)
{
@@ -3254,6 +3351,17 @@ public class Jalview2XML
.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());
+ }
+ }
}
}
@@ -3453,6 +3561,7 @@ public class Jalview2XML
view.getHeight());
af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
reorderAutoannotation(af, al, autoAlan);
+ af.alignPanel.alignmentChanged();
return af;
}
@@ -3701,6 +3810,20 @@ 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);
+ }
+ }
+ }
}
}
}
@@ -3727,11 +3850,11 @@ 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" : ""));
}