X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=e4435124d9e4d5f39b23dfdf92c275c1f4856ef8;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=28ac886cd43ccb8ffba122baf0112b8c8c93ef67;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 28ac886..e443512 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,44 +1,121 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.awt.Rectangle;
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
import java.lang.reflect.InvocationTargetException;
-import java.net.*;
-import java.util.*;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
import java.util.Map.Entry;
-import java.util.jar.*;
+import java.util.Set;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
-import javax.swing.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
-import org.exolab.castor.xml.*;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.schemabinding.version2.*;
-import jalview.schemes.*;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.schemabinding.version2.AlcodMap;
+import jalview.schemabinding.version2.AlcodonFrame;
+import jalview.schemabinding.version2.Annotation;
+import jalview.schemabinding.version2.AnnotationColours;
+import jalview.schemabinding.version2.AnnotationElement;
+import jalview.schemabinding.version2.CalcIdParam;
+import jalview.schemabinding.version2.DBRef;
+import jalview.schemabinding.version2.Features;
+import jalview.schemabinding.version2.Group;
+import jalview.schemabinding.version2.HiddenColumns;
+import jalview.schemabinding.version2.JGroup;
+import jalview.schemabinding.version2.JSeq;
+import jalview.schemabinding.version2.JalviewModel;
+import jalview.schemabinding.version2.JalviewModelSequence;
+import jalview.schemabinding.version2.MapListFrom;
+import jalview.schemabinding.version2.MapListTo;
+import jalview.schemabinding.version2.Mapping;
+import jalview.schemabinding.version2.MappingChoice;
+import jalview.schemabinding.version2.OtherData;
+import jalview.schemabinding.version2.PdbentryItem;
+import jalview.schemabinding.version2.Pdbids;
+import jalview.schemabinding.version2.Property;
+import jalview.schemabinding.version2.Sequence;
+import jalview.schemabinding.version2.SequenceSet;
+import jalview.schemabinding.version2.SequenceSetProperties;
+import jalview.schemabinding.version2.Setting;
+import jalview.schemabinding.version2.StructureState;
+import jalview.schemabinding.version2.ThresholdLine;
+import jalview.schemabinding.version2.Tree;
+import jalview.schemabinding.version2.UserColours;
+import jalview.schemabinding.version2.Viewport;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -58,6 +135,31 @@ import jalview.ws.params.WsParamSetI;
*/
public class Jalview2XML
{
+ private static final String UTF_8 = "UTF-8";
+
+ /*
+ * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
+ * of sequence objects are created.
+ */
+ IdentityHashMap seqsToIds = null;
+
+ /**
+ * jalview XML Sequence ID to jalview sequence object reference (both dataset
+ * and alignment sequences. Populated as XML reps of sequence objects are
+ * created.)
+ */
+ Map seqRefIds = null;
+
+ Vector frefedSequence = null;
+
+ boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+
+ /*
+ * Map of reconstructed AlignFrame objects that appear to have come from
+ * SplitFrame objects (have a dna/protein complement view).
+ */
+ private Map splitFrameCandidates = new HashMap();
+
/**
* create/return unique hash string for sq
*
@@ -72,7 +174,7 @@ public class Jalview2XML
}
if (seqsToIds.containsKey(sq))
{
- return (String) seqsToIds.get(sq);
+ return seqsToIds.get(sq);
}
else
{
@@ -113,31 +215,14 @@ public class Jalview2XML
{
if (seqsToIds == null)
{
- seqsToIds = new IdentityHashMap();
+ seqsToIds = new IdentityHashMap();
}
if (seqRefIds == null)
{
- seqRefIds = new Hashtable();
+ seqRefIds = new HashMap();
}
}
- /**
- * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
- * of sequence objects are created.
- */
- java.util.IdentityHashMap seqsToIds = null;
-
- /**
- * jalview XML Sequence ID to jalview sequence object reference (both dataset
- * and alignment sequences. Populated as XML reps of sequence objects are
- * created.)
- */
- java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
-
- Vector frefedSequence = null;
-
- boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
-
public Jalview2XML()
{
}
@@ -162,7 +247,7 @@ public class Jalview2XML
{
if (ref[1] instanceof jalview.datamodel.Mapping)
{
- SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ SequenceI seq = seqRefIds.get(sref);
while (seq.getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
@@ -173,7 +258,7 @@ public class Jalview2XML
{
if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
{
- SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ SequenceI seq = seqRefIds.get(sref);
while (seq.getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
@@ -223,28 +308,29 @@ public class Jalview2XML
}
/**
- * This maintains a list of viewports, the key being the seqSetId. Important
- * to set historyItem and redoList for multiple views
+ * This maintains a map of viewports, the key being the seqSetId. Important to
+ * set historyItem and redoList for multiple views
*/
- Hashtable viewportsAdded;
+ Map viewportsAdded = new HashMap();
- Hashtable annotationIds = new Hashtable();
+ Map annotationIds = new HashMap();
String uniqueSetSuffix = "";
/**
* List of pdbfiles added to Jar
*/
- Vector pdbfiles = null;
+ List pdbfiles = null;
// SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
- public void SaveState(File statefile)
+ public void saveState(File statefile)
{
+ FileOutputStream fos = null;
try
{
- FileOutputStream fos = new FileOutputStream(statefile);
+ fos = new FileOutputStream(statefile);
JarOutputStream jout = new JarOutputStream(fos);
- SaveState(jout);
+ saveState(jout);
} catch (Exception e)
{
@@ -260,6 +346,18 @@ public class Jalview2XML
errorMessage += "(output file was '" + statefile + "')";
}
e.printStackTrace();
+ } finally
+ {
+ if (fos != null)
+ {
+ try
+ {
+ fos.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
}
reportErrors();
}
@@ -269,83 +367,64 @@ public class Jalview2XML
*
* @param jout
*/
- public void SaveState(JarOutputStream jout)
+ public void saveState(JarOutputStream jout)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ AlignFrame[] frames = Desktop.getAlignFrames(); // Desktop.desktop.getAllFrames();
if (frames == null)
{
return;
}
+ Hashtable dsses = new Hashtable();
+
try
{
// NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
// //////////////////////////////////////////////////
- // NOTE ALSO new PrintWriter must be used for each new JarEntry
- PrintWriter out = null;
- Vector shortNames = new Vector();
+ List shortNames = new ArrayList();
// REVERSE ORDER
for (int i = frames.length - 1; i > -1; i--)
{
- if (frames[i] instanceof AlignFrame)
+ AlignFrame af = frames[i];
+ // skip ?
+ if (skipList != null
+ && skipList
+ .containsKey(af.getViewport().getSequenceSetId()))
{
- AlignFrame af = (AlignFrame) frames[i];
- // skip ?
- if (skipList != null
- && skipList.containsKey(af.getViewport()
- .getSequenceSetId()))
- {
- continue;
- }
-
- String shortName = af.getTitle();
+ continue;
+ }
- if (shortName.indexOf(File.separatorChar) > -1)
- {
- shortName = shortName.substring(shortName
- .lastIndexOf(File.separatorChar) + 1);
- }
+ String shortName = makeFilename(af, shortNames);
- int count = 1;
+ int ap, apSize = af.alignPanels.size();
- while (shortNames.contains(shortName))
+ for (ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = af.alignPanels.get(ap);
+ String fileName = apSize == 1 ? shortName : ap + shortName;
+ if (!fileName.endsWith(".xml"))
{
- if (shortName.endsWith("_" + (count - 1)))
- {
- shortName = shortName
- .substring(0, shortName.lastIndexOf("_"));
- }
-
- shortName = shortName.concat("_" + count);
- count++;
+ fileName = fileName + ".xml";
}
- shortNames.addElement(shortName);
+ saveState(apanel, fileName, jout);
- if (!shortName.endsWith(".xml"))
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
+ if (!dsses.containsKey(dssid))
{
- shortName = shortName + ".xml";
- }
-
- int ap, apSize = af.alignPanels.size();
- for (ap = 0; ap < apSize; ap++)
- {
- AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
- .elementAt(ap);
- String fileName = apSize == 1 ? shortName : ap + shortName;
- if (!fileName.endsWith(".xml"))
- {
- fileName = fileName + ".xml";
- }
-
- SaveState(apanel, fileName, jout);
+ dsses.put(dssid, af);
}
}
}
+
+ writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
+ jout);
+
try
{
jout.flush();
@@ -366,27 +445,75 @@ public class Jalview2XML
}
}
+ /**
+ * Generates a distinct file name, based on the title of the AlignFrame, by
+ * appending _n for increasing n until an unused name is generated. The new
+ * name (without its extension) is added to the list.
+ *
+ * @param af
+ * @param namesUsed
+ * @return the generated name, with .xml extension
+ */
+ protected String makeFilename(AlignFrame af, List namesUsed)
+ {
+ String shortName = af.getTitle();
+
+ if (shortName.indexOf(File.separatorChar) > -1)
+ {
+ shortName = shortName.substring(shortName
+ .lastIndexOf(File.separatorChar) + 1);
+ }
+
+ int count = 1;
+
+ while (namesUsed.contains(shortName))
+ {
+ if (shortName.endsWith("_" + (count - 1)))
+ {
+ shortName = shortName.substring(0, shortName.lastIndexOf("_"));
+ }
+
+ shortName = shortName.concat("_" + count);
+ count++;
+ }
+
+ namesUsed.add(shortName);
+
+ if (!shortName.endsWith(".xml"))
+ {
+ shortName = shortName + ".xml";
+ }
+ return shortName;
+ }
+
// USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
- public boolean SaveAlignment(AlignFrame af, String jarFile,
+ public boolean saveAlignment(AlignFrame af, String jarFile,
String fileName)
{
try
{
- int ap, apSize = af.alignPanels.size();
+ int ap = 0;
+ int apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
- for (ap = 0; ap < apSize; ap++)
+ Hashtable dsses = new Hashtable();
+ for (AlignmentPanel apanel : af.alignPanels)
{
- AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
- .elementAt(ap);
String jfileName = apSize == 1 ? fileName : fileName + ap;
+ ap++;
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
}
- SaveState(apanel, jfileName, jout);
+ 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();
@@ -404,8 +531,24 @@ 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
+ * create a JalviewModel from an alignment view and marshall it to a
* JarOutputStream
*
* @param ap
@@ -417,12 +560,34 @@ public class Jalview2XML
* @param out
* jar entry name
*/
- public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+ public JalviewModel saveState(AlignmentPanel ap, String fileName,
JarOutputStream jout)
{
+ return saveState(ap, fileName, false, jout);
+ }
+
+ /**
+ * create a JalviewModel from an alignment 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();
+ List viewIds = new ArrayList();
+ List userColours = new ArrayList();
AlignViewport av = ap.av;
@@ -430,7 +595,8 @@ public class Jalview2XML
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- object.setVersion(jalview.bin.Cache.getDefault("VERSION","Development Build"));
+ object.setVersion(jalview.bin.Cache.getDefault("VERSION",
+ "Development Build"));
jalview.datamodel.AlignmentI jal = av.getAlignment();
@@ -449,6 +615,11 @@ 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 +639,12 @@ 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 +676,34 @@ 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 (jds.getSequenceFeatures() != null)
{
- jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
+ jalview.datamodel.SequenceFeature[] sf = jds
.getSequenceFeatures();
int index = 0;
while (index < sf.length)
@@ -567,84 +745,50 @@ 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();
jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
.nextElement();
- pdb.setId(entry.getId());
+ String pdbId = entry.getId();
+ pdb.setId(pdbId);
pdb.setType(entry.getType());
- AppJmol jmol;
+ /*
+ * Store any structure views associated with this sequence. This
+ * section copes with duplicate entries in the project, so a dataset
+ * only view *should* be coped with sensibly.
+ */
// This must have been loaded, is it still visible?
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
String matchedFile = null;
for (int f = frames.length - 1; f > -1; f--)
{
- if (frames[f] instanceof AppJmol)
+ if (frames[f] instanceof StructureViewerBase)
{
- jmol = (AppJmol) frames[f];
- for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++)
+ StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
+ matchedFile = saveStructureState(ap, jds, pdb, entry,
+ viewIds, matchedFile, viewFrame);
+ /*
+ * Only store each structure viewer's state once in each XML
+ * document. First time through only (storeDS==false)
+ */
+ String viewId = viewFrame.getViewId();
+ if (!storeDS && !viewIds.contains(viewId))
{
- if (!jmol.jmb.pdbentry[peid].getId().equals(entry.getId())
- && !(entry.getId().length() > 4 && entry
- .getId()
- .toLowerCase()
- .startsWith(
- jmol.jmb.pdbentry[peid].getId()
- .toLowerCase())))
- continue;
- if (matchedFile == null)
+ viewIds.add(viewId);
+ try
{
- matchedFile = jmol.jmb.pdbentry[peid].getFile();
- }
- else if (!matchedFile.equals(jmol.jmb.pdbentry[peid]
- .getFile()))
+ writeJarEntry(jout, getViewerJarEntryName(viewId),
+ viewFrame.getStateInfo().getBytes());
+ } catch (IOException e)
{
- Cache.log
- .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
- + jmol.jmb.pdbentry[peid].getFile());
- ; // record the
- }
- // file so we
- // can get at it if the ID
- // match is ambiguous (e.g.
- // 1QIP==1qipA)
- String statestring = jmol.jmb.viewer.getStateInfo();
-
- 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])
- {
- StructureState state = new StructureState();
- state.setVisible(true);
- state.setXpos(jmol.getX());
- state.setYpos(jmol.getY());
- state.setWidth(jmol.getWidth());
- state.setHeight(jmol.getHeight());
- state.setViewId(jmol.getViewId());
- state.setAlignwithAlignPanel(jmol.isUsedforaligment(ap));
- state.setColourwithAlignPanel(jmol
- .isUsedforcolourby(ap));
- state.setColourByJmol(jmol.isColouredByJmol());
- if (!jmolViewIds.contains(state.getViewId()))
- {
- // Make sure we only store a Jmol state once in each XML
- // document.
- jmolViewIds.addElement(state.getViewId());
- state.setContent(statestring.replaceAll("\n", ""));
- }
- else
- {
- state.setContent("# duplicate state");
- }
- pdb.addStructureState(state);
- }
+ System.err.println("Error saving viewer state: "
+ + e.getMessage());
}
}
}
@@ -660,37 +804,17 @@ public class Jalview2XML
pdb.setFile(matchedFile); // entry.getFile());
if (pdbfiles == null)
{
- pdbfiles = new Vector();
+ pdbfiles = new ArrayList();
}
- if (!pdbfiles.contains(entry.getId()))
+ if (!pdbfiles.contains(pdbId))
{
- pdbfiles.addElement(entry.getId());
- try
- {
- File file = new File(matchedFile);
- if (file.exists() && jout != null)
- {
- byte[] data = new byte[(int) file.length()];
- jout.putNextEntry(new JarEntry(entry.getId()));
- DataInputStream dis = new DataInputStream(
- new FileInputStream(file));
- dis.readFully(data);
-
- DataOutputStream dout = new DataOutputStream(jout);
- dout.write(data, 0, data.length);
- dout.flush();
- jout.closeEntry();
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
+ pdbfiles.add(pdbId);
+ copyFileToJar(jout, matchedFile, pdbId);
}
}
- if (entry.getProperty() != null)
+ if (entry.getProperty() != null && !entry.getProperty().isEmpty())
{
PdbentryItem item = new PdbentryItem();
Hashtable properties = entry.getProperty();
@@ -713,36 +837,23 @@ public class Jalview2XML
jms.addJSeq(jseq);
}
- if (av.hasHiddenRows())
+ if (!storeDS && av.hasHiddenRows())
{
jal = av.getAlignment();
}
// SAVE MAPPINGS
- if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
+ if (jal.getCodonFrames() != null)
{
- jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
- for (int i = 0; i < jac.length; i++)
+ Set jac = jal.getCodonFrames();
+ for (AlignedCodonFrame acf : jac)
{
AlcodonFrame alc = new AlcodonFrame();
vamsasSet.addAlcodonFrame(alc);
- for (int p = 0; p < jac[i].aaWidth; p++)
+ if (acf.getProtMappings() != null
+ && acf.getProtMappings().length > 0)
{
- Alcodon cmap = new Alcodon();
- if (jac[i].codons[p] != null)
- {
- // Null codons indicate a gapped column in the translated peptide
- // alignment.
- cmap.setPos1(jac[i].codons[p][0]);
- cmap.setPos2(jac[i].codons[p][1]);
- cmap.setPos3(jac[i].codons[p][2]);
- }
- alc.addAlcodon(cmap);
- }
- if (jac[i].getProtMappings() != null
- && jac[i].getProtMappings().length > 0)
- {
- SequenceI[] dnas = jac[i].getdnaSeqs();
- jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
+ SequenceI[] dnas = acf.getdnaSeqs();
+ jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
for (int m = 0; m < pmaps.length; m++)
{
AlcodMap alcmap = new AlcodMap();
@@ -752,12 +863,43 @@ public class Jalview2XML
alc.addAlcodMap(alcmap);
}
}
+
+// {
+// AlcodonFrame alc = new AlcodonFrame();
+// vamsasSet.addAlcodonFrame(alc);
+// for (int p = 0; p < acf.aaWidth; p++)
+// {
+// Alcodon cmap = new Alcodon();
+// if (acf.codons[p] != null)
+// {
+// // Null codons indicate a gapped column in the translated peptide
+// // alignment.
+// cmap.setPos1(acf.codons[p][0]);
+// cmap.setPos2(acf.codons[p][1]);
+// cmap.setPos3(acf.codons[p][2]);
+// }
+// alc.addAlcodon(cmap);
+// }
+// if (acf.getProtMappings() != null
+// && acf.getProtMappings().length > 0)
+// {
+// SequenceI[] dnas = acf.getdnaSeqs();
+// jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
+// for (int m = 0; m < pmaps.length; m++)
+// {
+// AlcodMap alcmap = new AlcodMap();
+// alcmap.setDnasq(seqHash(dnas[m]));
+// alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
+// false));
+// alc.addAlcodMap(alcmap);
+// }
+// }
}
}
// SAVE TREES
// /////////////////////////////////
- if (av.currentTree != null)
+ if (!storeDS && av.currentTree != null)
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
@@ -799,144 +941,52 @@ public class Jalview2XML
}
}
}
- // SAVE ANNOTATIONS
- /**
- * store forward refs from an annotationRow to any groups
+
+ /*
+ * Save associated Varna panels
*/
- IdentityHashMap groupRefs = new IdentityHashMap();
- if (jal.getAlignmentAnnotation() != null)
+ if (Desktop.desktop != null)
{
- jalview.datamodel.AlignmentAnnotation[] aa = jal
- .getAlignmentAnnotation();
-
- for (int i = 0; i < aa.length; i++)
+ for (JInternalFrame frame : Desktop.desktop.getAllFrames())
{
- Annotation an = new Annotation();
-
- if (aa[i].annotationId != null)
+ if (frame instanceof AppVarna)
{
- 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)
+ AppVarna vp = (AppVarna) frame;
+ if (vp.ap == ap)
{
- // make a locally unique String
- groupRefs.put(aa[i].groupRef,
- groupIdr = ("" + System.currentTimeMillis()
- + aa[i].groupRef.getName() + groupRefs.size()));
+ // save Varna state
}
- 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
+ // SAVE ANNOTATIONS
+ /**
+ * store forward refs from an annotationRow to any groups
+ */
+ IdentityHashMap groupRefs = new IdentityHashMap();
+ if (storeDS)
+ {
+ for (SequenceI sq : jal.getSequences())
+ {
+ // Store annotation on dataset sequences only
+ jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation();
+ if (aa != null && aa.length > 0)
{
- an.setScoreOnly(true);
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
}
- 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
@@ -964,7 +1014,7 @@ public class Jalview2XML
if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
- groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+ groups[i].setColour(setUserColourScheme(sg.cs, userColours,
jms));
}
else
@@ -975,15 +1025,15 @@ 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)
{
groups[i]
- .setColour(SetUserColourScheme(sg.cs, userColours, jms));
+ .setColour(setUserColourScheme(sg.cs, userColours, jms));
}
else
{
@@ -1015,253 +1065,241 @@ 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());
+ if (av.getCodingComplement() != null)
+ {
+ view.setComplementId(av.getCodingComplement().getViewId());
+ }
+ view.setViewName(av.viewName);
+ view.setGatheredViews(av.isGatherViewsHere());
- // /////////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);
+ Rectangle position = ap.av.getExplodedGeometry();
+ if (position == null)
+ {
+ position = ap.alignFrame.getBounds();
+ }
+ view.setXpos(position.x);
+ view.setYpos(position.y);
+ view.setWidth(position.width);
+ view.setHeight(position.height);
- 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());
- ac.setPerSequence(acg.isSeqAssociated());
- ac.setPredefinedColours(acg.isPredefinedColours());
- 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.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++)
- {
- gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getFeatureStyle(renderOrder[ro]);
- Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
- if (gstyle instanceof GraduatedColor)
+ 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.isRenderGaps());
+ view.setShowAnnotation(av.isShowAnnotation());
+ view.setShowBoxes(av.getShowBoxes());
+ view.setShowColourText(av.getColourText());
+ view.setShowFullId(av.getShowJVSuffix());
+ view.setRightAlignIds(av.isRightAlignIds());
+ view.setShowSequenceFeatures(av.isShowSequenceFeatures());
+ view.setShowText(av.getShowText());
+ view.setShowUnconserved(av.getShowUnconserved());
+ view.setWrapAlignment(av.getWrapAlignment());
+ view.setTextCol1(av.getTextColour().getRGB());
+ view.setTextCol2(av.getTextColour2().getRGB());
+ view.setTextColThreshold(av.getThresholdTextColour());
+ 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.isFollowHighlight());
+ view.setFollowSelection(av.followSelection);
+ view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
+ if (av.getFeaturesDisplayed() != null)
+ {
+ jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
+
+ String[] renderOrder = ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer().getRenderOrder()
+ .toArray(new String[0]);
+
+ Vector settingsAdded = new Vector();
+ Object gstyle = null;
+ GraduatedColor gcol = null;
+ if (renderOrder != null)
+ {
+ 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.getSeqPanel().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.getSeqPanel().seqCanvas
+ .getFeatureRenderer()
+ .getColour(renderOrder[ro]).getRGB());
+ }
+
+ setting.setDisplay(av.getFeaturesDisplayed().isVisible(
+ renderOrder[ro]));
+ float rorder = ap.getSeqPanel().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.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getFeatureColours().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]));
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getOrder(renderOrder[ro]);
+ Setting setting = new Setting();
+ setting.setType(key);
+ setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getColour(key).getRGB());
+
+ setting.setDisplay(false);
+ float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .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))
+ // is groups actually supposed to be a map here ?
+ en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getFeatureGroups().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.getSeqPanel().seqCanvas
+ .getFeatureRenderer().checkGroupVisibility(grp, false))
+ .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 = av.getColumnSelection().getHiddenColumns()
+ .get(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);
@@ -1275,9 +1313,8 @@ public class Jalview2XML
JarEntry entry = new JarEntry(fileName);
jout.putNextEntry(entry);
PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
- org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
- pout);
+ UTF_8));
+ Marshaller marshaller = new Marshaller(pout);
marshaller.marshal(object);
pout.flush();
jout.closeEntry();
@@ -1290,6 +1327,327 @@ public class Jalview2XML
return object;
}
+ /**
+ * Copy the contents of a file to a new file added to the output jar
+ *
+ * @param jout
+ * @param infilePath
+ * @param jarfileName
+ */
+ protected void copyFileToJar(JarOutputStream jout, String infilePath,
+ String jarfileName)
+ {
+ DataInputStream dis = null;
+ try
+ {
+ File file = new File(infilePath);
+ if (file.exists() && jout != null)
+ {
+ dis = new DataInputStream(new FileInputStream(file));
+ byte[] data = new byte[(int) file.length()];
+ dis.readFully(data);
+ writeJarEntry(jout, jarfileName, data);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (dis != null)
+ {
+ try
+ {
+ dis.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+
+ /**
+ * Write the data to a new entry of given name in the output jar file
+ *
+ * @param jout
+ * @param jarfileName
+ * @param data
+ * @throws IOException
+ */
+ protected void writeJarEntry(JarOutputStream jout, String jarfileName,
+ byte[] data) throws IOException
+ {
+ if (jout != null)
+ {
+ jout.putNextEntry(new JarEntry(jarfileName));
+ DataOutputStream dout = new DataOutputStream(jout);
+ dout.write(data, 0, data.length);
+ dout.flush();
+ jout.closeEntry();
+ }
+ }
+
+ /**
+ * Save the state of a structure viewer
+ *
+ * @param ap
+ * @param jds
+ * @param pdb
+ * the archive XML element under which to save the state
+ * @param entry
+ * @param viewIds
+ * @param matchedFile
+ * @param viewFrame
+ * @return
+ */
+ protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
+ Pdbids pdb, PDBEntry entry, List viewIds,
+ String matchedFile, StructureViewerBase viewFrame)
+ {
+ final AAStructureBindingModel bindingModel = viewFrame.getBinding();
+
+ /*
+ * Look for any bindings for this viewer to the PDB file of interest
+ * (including part matches excluding chain id)
+ */
+ for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
+ {
+ final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
+ final String pdbId = pdbentry.getId();
+ if (!pdbId.equals(entry.getId())
+ && !(entry.getId().length() > 4 && entry.getId()
+ .toLowerCase().startsWith(pdbId.toLowerCase())))
+ {
+ /*
+ * not interested in a binding to a different PDB entry here
+ */
+ continue;
+ }
+ if (matchedFile == null)
+ {
+ matchedFile = pdbentry.getFile();
+ }
+ else if (!matchedFile.equals(pdbentry.getFile()))
+ {
+ Cache.log
+ .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ + pdbentry.getFile());
+ }
+ // record the
+ // file so we
+ // can get at it if the ID
+ // match is ambiguous (e.g.
+ // 1QIP==1qipA)
+
+ for (int smap = 0; smap < viewFrame.getBinding().getSequence()[peid].length; smap++)
+ {
+ // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+ if (jds == viewFrame.getBinding().getSequence()[peid][smap])
+ {
+ StructureState state = new StructureState();
+ state.setVisible(true);
+ state.setXpos(viewFrame.getX());
+ state.setYpos(viewFrame.getY());
+ state.setWidth(viewFrame.getWidth());
+ state.setHeight(viewFrame.getHeight());
+ final String viewId = viewFrame.getViewId();
+ state.setViewId(viewId);
+ state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
+ state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
+ state.setColourByJmol(viewFrame.isColouredByViewer());
+ state.setType(viewFrame.getViewerType().toString());
+ pdb.addStructureState(state);
+ }
+ }
+ }
+ return matchedFile;
+ }
+
+ private AnnotationColours constructAnnotationColours(
+ AnnotationColourGradient acg, List 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());
+ }
+ if (aa[i].hasProperties())
+ {
+ for (String pr : aa[i].getProperties())
+ {
+ Property prop = new Property();
+ prop.setName(pr);
+ prop.setValue(aa[i].getProperty(pr));
+ an.addProperty(prop);
+ }
+ }
+
+ 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 > ' ')
+ {
+ 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);
@@ -1379,8 +1737,9 @@ public class Jalview2XML
return false;
}
}
- throw new Error("Unsupported Version for calcIdparam "
- + calcIdParam.toString());
+ throw new Error(MessageManager.formatMessage(
+ "error.unsupported_version_calcIdparam", new Object[]
+ { calcIdParam.toString() }));
}
/**
@@ -1502,20 +1861,20 @@ public class Jalview2XML
mp = new Mapping();
jalview.util.MapList mlst = jmp.getMap();
- int r[] = mlst.getFromRanges();
- for (int s = 0; s < r.length; s += 2)
+ List r = mlst.getFromRanges();
+ for (int[] range : r)
{
MapListFrom mfrom = new MapListFrom();
- mfrom.setStart(r[s]);
- mfrom.setEnd(r[s + 1]);
+ mfrom.setStart(range[0]);
+ mfrom.setEnd(range[1]);
mp.addMapListFrom(mfrom);
}
r = mlst.getToRanges();
- for (int s = 0; s < r.length; s += 2)
+ for (int[] range : r)
{
MapListTo mto = new MapListTo();
- mto.setStart(r[s]);
- mto.setEnd(r[s + 1]);
+ mto.setStart(range[0]);
+ mto.setEnd(range[1]);
mp.addMapListTo(mto);
}
mp.setMapFromUnit(mlst.getFromRatio());
@@ -1561,8 +1920,8 @@ public class Jalview2XML
return mp;
}
- String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
- Vector userColours, JalviewModelSequence jms)
+ String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
+ List userColours, JalviewModelSequence jms)
{
String id = null;
jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
@@ -1607,7 +1966,7 @@ public class Jalview2XML
return id;
}
- jalview.schemes.UserColourScheme GetUserColourScheme(
+ jalview.schemes.UserColourScheme getUserColourScheme(
JalviewModelSequence jms, String id)
{
UserColours[] uc = jms.getUserColours();
@@ -1665,7 +2024,7 @@ public class Jalview2XML
* @param file
* - HTTP URL or filename
*/
- public AlignFrame LoadJalviewAlign(final String file)
+ public AlignFrame loadJalviewAlign(final String file)
{
jalview.gui.AlignFrame af = null;
@@ -1673,21 +2032,21 @@ public class Jalview2XML
try
{
// create list to store references for any new Jmol viewers created
- newStructureViewers=new Vector();
+ newStructureViewers = new Vector();
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
// so we can re-open the jar input stream for each entry.
jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
- af = LoadJalviewAlign(jprovider);
-
+ af = loadJalviewAlign(jprovider);
+
} catch (MalformedURLException e)
{
errorMessage = "Invalid URL format for '" + file + "'";
reportErrors();
- }
- finally {
+ } finally
+ {
try
{
SwingUtilities.invokeAndWait(new Runnable()
@@ -1712,7 +2071,7 @@ public class Jalview2XML
errorMessage = null;
uniqueSetSuffix = null;
seqRefIds = null;
- viewportsAdded = null;
+ viewportsAdded.clear();
frefedSequence = null;
if (file.startsWith("http://"))
@@ -1753,7 +2112,7 @@ public class Jalview2XML
* @param jprovider
* @return
*/
- public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
+ public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
{
errorMessage = null;
if (uniqueSetSuffix == null)
@@ -1762,19 +2121,15 @@ public class Jalview2XML
}
if (seqRefIds == null)
{
- seqRefIds = new Hashtable();
- }
- if (viewportsAdded == null)
- {
- viewportsAdded = new Hashtable();
+ seqRefIds = new HashMap();
}
if (frefedSequence == null)
{
frefedSequence = new Vector();
}
- jalview.gui.AlignFrame af = null;
- Hashtable gatherToThisFrame = new Hashtable();
+ AlignFrame af = null, _af = null;
+ Map gatherToThisFrame = new HashMap();
final String file = jprovider.getFilename();
try
{
@@ -1792,7 +2147,7 @@ public class Jalview2XML
if (jarentry != null && jarentry.getName().endsWith(".xml"))
{
- InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+ InputStreamReader in = new InputStreamReader(jin, UTF_8);
JalviewModel object = new JalviewModel();
Unmarshaller unmar = new Unmarshaller(object);
@@ -1800,10 +2155,14 @@ 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.isGatherViewsHere())
+ {
+ gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ }
}
}
entryCount++;
@@ -1870,16 +2229,128 @@ public class Jalview2XML
Desktop.instance.stopLoading();
}
- Enumeration en = gatherToThisFrame.elements();
- while (en.hasMoreElements())
- {
- Desktop.instance.gatherViews((AlignFrame) en.nextElement());
- }
- if (errorMessage != null)
- {
- reportErrors();
- }
- return af;
+ /*
+ * Regather multiple views (with the same sequence set id) to the frame (if
+ * any) that is flagged as the one to gather to, i.e. convert them to tabbed
+ * views instead of separate frames. Note this doesn't restore a state where
+ * some expanded views in turn have tabbed views - the last "first tab" read
+ * in will play the role of gatherer for all.
+ */
+ for (AlignFrame fr : gatherToThisFrame.values())
+ {
+ Desktop.instance.gatherViews(fr);
+ }
+
+ restoreSplitFrames();
+
+ if (errorMessage != null)
+ {
+ reportErrors();
+ }
+ return af;
+ }
+
+ /**
+ * Try to reconstruct and display SplitFrame windows, where each contains
+ * complementary dna and protein alignments. Done by pairing up AlignFrame
+ * objects (created earlier) which have complementary viewport ids associated.
+ */
+ protected void restoreSplitFrames()
+ {
+ List gatherTo = new ArrayList();
+ List addedToSplitFrames = new ArrayList();
+ Map dna = new HashMap();
+
+ /*
+ * Identify the DNA alignments
+ */
+ for (Entry candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (af.getViewport().getAlignment().isNucleotide())
+ {
+ dna.put(candidate.getKey().getId(), af);
+ }
+ }
+
+ /*
+ * Try to match up the protein complements
+ */
+ for (Entry candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (!af.getViewport().getAlignment().isNucleotide())
+ {
+ String complementId = candidate.getKey().getComplementId();
+ // only non-null complements should be in the Map
+ if (complementId != null && dna.containsKey(complementId))
+ {
+ final AlignFrame dnaFrame = dna.get(complementId);
+ SplitFrame sf = createSplitFrame(dnaFrame, af);
+ addedToSplitFrames.add(dnaFrame);
+ addedToSplitFrames.add(af);
+ if (af.viewport.isGatherViewsHere())
+ {
+ gatherTo.add(sf);
+ }
+ }
+ }
+ }
+
+ /*
+ * Open any that we failed to pair up (which shouldn't happen!) as
+ * standalone AlignFrame's.
+ */
+ for (Entry candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (!addedToSplitFrames.contains(af)) {
+ Viewport view = candidate.getKey();
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+ view.getHeight());
+ System.err.println("Failed to restore view " + view.getTitle()
+ + " to split frame");
+ }
+ }
+
+ /*
+ * Gather back into tabbed views as flagged.
+ */
+ for (SplitFrame sf : gatherTo)
+ {
+ Desktop.instance.gatherViews(sf);
+ }
+
+ splitFrameCandidates.clear();
+ }
+
+ /**
+ * Construct and display one SplitFrame holding DNA and protein alignments.
+ *
+ * @param dnaFrame
+ * @param proteinFrame
+ * @return
+ */
+ protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
+ AlignFrame proteinFrame)
+ {
+ SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
+ String title = MessageManager.getString("label.linked_view_title");
+ int width = (int) dnaFrame.getBounds().getWidth();
+ int height = (int) (dnaFrame.getBounds().getHeight()
+ + proteinFrame.getBounds().getHeight() + 50);
+ Desktop.addInternalFrame(splitFrame, title, width, height);
+
+ /*
+ * And compute cDNA consensus (couldn't do earlier with consensus as
+ * mappings were not yet present)
+ */
+ proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
+
+ return splitFrame;
}
/**
@@ -1919,7 +2390,7 @@ public class Jalview2XML
errorMessage = null;
}
- Hashtable alreadyLoadedPDB;
+ Map alreadyLoadedPDB = new HashMap();
/**
* when set, local views will be updated from view stored in JalviewXML
@@ -1928,13 +2399,47 @@ public class Jalview2XML
*/
private final boolean updateLocalViews = false;
+ /**
+ * Returns the path to a temporary file holding the PDB file for the given PDB
+ * id. The first time of asking, searches for a file of that name in the
+ * Jalview project jar, and copies it to a new temporary file. Any repeat
+ * requests just return the path to the file previously created.
+ *
+ * @param jprovider
+ * @param pdbId
+ * @return
+ */
String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
{
- if (alreadyLoadedPDB == null)
- alreadyLoadedPDB = new Hashtable();
-
if (alreadyLoadedPDB.containsKey(pdbId))
+ {
return alreadyLoadedPDB.get(pdbId).toString();
+ }
+
+ String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
+ if (tempFile != null)
+ {
+ alreadyLoadedPDB.put(pdbId, tempFile);
+ }
+ return tempFile;
+ }
+
+ /**
+ * Copies the jar entry of given name to a new temporary file and returns the
+ * path to the file, or null if the entry is not found.
+ *
+ * @param jprovider
+ * @param jarEntryName
+ * @param prefix
+ * a prefix for the temporary file name, must be at least three
+ * characters long
+ * @return
+ */
+ protected String copyJarEntry(jarInputStreamProvider jprovider,
+ String jarEntryName, String prefix)
+ {
+ BufferedReader in = null;
+ PrintWriter out = null;
try
{
@@ -1949,38 +2454,46 @@ public class Jalview2XML
do
{
entry = jin.getNextJarEntry();
- } while (entry != null && !entry.getName().equals(pdbId));
+ } while (entry != null && !entry.getName().equals(jarEntryName));
if (entry != null)
{
- BufferedReader in = new BufferedReader(new InputStreamReader(jin));
- File outFile = File.createTempFile("jalview_pdb", ".txt");
+ in = new BufferedReader(new InputStreamReader(jin, UTF_8));
+ File outFile = File.createTempFile(prefix, ".tmp");
outFile.deleteOnExit();
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ out = new PrintWriter(new FileOutputStream(outFile));
String data;
while ((data = in.readLine()) != null)
{
out.println(data);
}
- try
- {
- out.flush();
- } catch (Exception foo)
- {
- }
- ;
- out.close();
+ out.flush();
String t = outFile.getAbsolutePath();
- alreadyLoadedPDB.put(pdbId, t);
return t;
}
else
{
- warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
+ warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
}
} catch (Exception ex)
{
ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ if (out != null)
+ {
+ out.close();
+ }
}
return null;
@@ -2018,7 +2531,7 @@ public class Jalview2XML
* data source provider
* @return alignment frame created from view stored in DOM
*/
- AlignFrame LoadFromObject(JalviewModel object, String file,
+ AlignFrame loadFromObject(JalviewModel object, String file,
boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
@@ -2026,22 +2539,24 @@ public class Jalview2XML
JalviewModelSequence jms = object.getJalviewModelSequence();
- Viewport view = jms.getViewport(0);
+ Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
+ : null;
+
// ////////////////////////////////
// LOAD SEQUENCES
- Vector hiddenSeqs = null;
+ List hiddenSeqs = null;
jalview.datamodel.Sequence jseq;
- ArrayList tmpseqs = new ArrayList();
+ List tmpseqs = new ArrayList();
boolean multipleView = false;
- JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+ JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
int vi = 0; // counter in vamsasSeq array
- for (int i = 0; i < JSEQ.length; i++)
+ for (int i = 0; i < jseqs.length; i++)
{
- String seqId = JSEQ[i].getId();
+ String seqId = jseqs[i].getId();
if (seqRefIds.get(seqId) != null)
{
@@ -2053,22 +2568,22 @@ public class Jalview2XML
jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
vamsasSeq[vi].getSequence());
jseq.setDescription(vamsasSeq[vi].getDescription());
- jseq.setStart(JSEQ[i].getStart());
- jseq.setEnd(JSEQ[i].getEnd());
+ jseq.setStart(jseqs[i].getStart());
+ jseq.setEnd(jseqs[i].getEnd());
jseq.setVamsasId(uniqueSetSuffix + seqId);
seqRefIds.put(vamsasSeq[vi].getId(), jseq);
tmpseqs.add(jseq);
vi++;
}
- if (JSEQ[i].getHidden())
+ if (jseqs[i].getHidden())
{
if (hiddenSeqs == null)
{
- hiddenSeqs = new Vector();
+ hiddenSeqs = new ArrayList();
}
- hiddenSeqs.addElement(seqRefIds.get(seqId));
+ hiddenSeqs.add(seqRefIds.get(seqId));
}
}
@@ -2076,13 +2591,10 @@ public class Jalview2XML
// /
// Create the alignment object from the sequence set
// ///////////////////////////////
- jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
- .size()];
-
- tmpseqs.toArray(orderedSeqs);
+ SequenceI[] orderedSeqs = tmpseqs
+ .toArray(new SequenceI[tmpseqs.size()]);
- jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
- orderedSeqs);
+ Alignment al = new Alignment(orderedSeqs);
// / Add the alignment properties
for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
@@ -2102,20 +2614,23 @@ public class Jalview2XML
}
else
{
- recoverDatasetFor(vamsasSet, al);
+ // recover dataset - passing on flag indicating if this a 'viewless'
+ // sequence set (a.k.a. a stored dataset for the project)
+ recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
+ .getViewportCount() == 0);
}
// ///////////////////////////////
- Hashtable pdbloaded = new Hashtable();
+ Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
if (!multipleView)
{
// load sequence features, database references and any associated PDB
// structures for the alignment
for (int i = 0; i < vamsasSeq.length; i++)
{
- if (JSEQ[i].getFeaturesCount() > 0)
+ if (jseqs[i].getFeaturesCount() > 0)
{
- Features[] features = JSEQ[i].getFeatures();
+ Features[] features = jseqs[i].getFeatures();
for (int f = 0; f < features.length; f++)
{
jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
@@ -2145,14 +2660,24 @@ public class Jalview2XML
{
addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
}
- if (JSEQ[i].getPdbidsCount() > 0)
+ if (jseqs[i].getPdbidsCount() > 0)
{
- Pdbids[] ids = JSEQ[i].getPdbids();
+ Pdbids[] ids = jseqs[i].getPdbids();
for (int p = 0; p < ids.length; p++)
{
jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
entry.setId(ids[p].getId());
- entry.setType(ids[p].getType());
+ if (ids[p].getType() != null)
+ {
+ if (ids[p].getType().equalsIgnoreCase("PDB"))
+ {
+ entry.setType(PDBEntry.Type.PDB);
+ }
+ else
+ {
+ entry.setType(PDBEntry.Type.FILE);
+ }
+ }
if (ids[p].getFile() != null)
{
if (!pdbloaded.containsKey(ids[p].getFile()))
@@ -2164,7 +2689,8 @@ public class Jalview2XML
entry.setFile(pdbloaded.get(ids[p].getId()).toString());
}
}
-
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(entry);
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
}
}
@@ -2181,35 +2707,13 @@ public class Jalview2XML
AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
for (int i = 0; i < alc.length; i++)
{
- jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
- alc[i].getAlcodonCount());
- if (alc[i].getAlcodonCount() > 0)
- {
- Alcodon[] alcods = alc[i].getAlcodon();
- for (int p = 0; p < cf.codons.length; p++)
- {
- if (alcods[p].hasPos1() && alcods[p].hasPos2()
- && alcods[p].hasPos3())
- {
- // translated codons require three valid positions
- cf.codons[p] = new int[3];
- cf.codons[p][0] = (int) alcods[p].getPos1();
- cf.codons[p][1] = (int) alcods[p].getPos2();
- cf.codons[p][2] = (int) alcods[p].getPos3();
- }
- else
- {
- cf.codons[p] = null;
- }
- }
- }
+ AlignedCodonFrame cf = new AlignedCodonFrame();
if (alc[i].getAlcodMapCount() > 0)
{
AlcodMap[] maps = alc[i].getAlcodMap();
for (int m = 0; m < maps.length; m++)
{
- SequenceI dnaseq = (SequenceI) seqRefIds
- .get(maps[m].getDnasq());
+ SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
// Load Mapping
jalview.datamodel.Mapping mapping = null;
// attach to dna sequence reference.
@@ -2231,12 +2735,11 @@ public class Jalview2XML
}
al.addCodonFrame(cf);
}
-
}
// ////////////////////////////////
// LOAD ANNOTATIONS
- ArrayList autoAlan = new ArrayList();
+ List autoAlan = new ArrayList();
/**
* store any annotations which forward reference a group's ID
*/
@@ -2275,12 +2778,13 @@ public class Jalview2XML
if (an[i].getId() != null
&& annotationIds.containsKey(an[i].getId()))
{
- jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
- .get(an[i].getId());
+ AlignmentAnnotation jda = annotationIds.get(an[i].getId());
// in principle Visible should always be true for annotation displayed
// in multiple views
if (an[i].hasVisible())
+ {
jda.visible = an[i].getVisible();
+ }
al.addAnnotation(jda);
@@ -2299,7 +2803,9 @@ public class Jalview2XML
anpos = ae[aa].getPosition();
if (anpos >= anot.length)
+ {
continue;
+ }
anot[anpos] = new jalview.datamodel.Annotation(
@@ -2393,10 +2899,14 @@ public class Jalview2XML
jaa.setScore(an[i].getScore());
}
if (an[i].hasVisible())
+ {
jaa.visible = an[i].getVisible();
+ }
if (an[i].hasCentreColLabels())
+ {
jaa.centreColLabels = an[i].getCentreColLabels();
+ }
if (an[i].hasScaleColLabels())
{
@@ -2418,7 +2928,14 @@ public class Jalview2XML
jaa.belowAlignment = an[i].isBelowAlignment();
}
jaa.setCalcId(an[i].getCalcId());
-
+ if (an[i].getPropertyCount() > 0)
+ {
+ for (jalview.schemabinding.version2.Property prop : an[i]
+ .getProperty())
+ {
+ jaa.setProperty(prop.getName(), prop.getValue());
+ }
+ }
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
@@ -2432,14 +2949,13 @@ 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;
@@ -2448,7 +2964,13 @@ public class Jalview2XML
{
if (groups[i].getColour().startsWith("ucs"))
{
- cs = GetUserColourScheme(jms, groups[i].getColour());
+ cs = getUserColourScheme(jms, groups[i].getColour());
+ }
+ else if (groups[i].getColour().equals("AnnotationColourGradient")
+ && groups[i].getAnnotationColours() != null)
+ {
+ addAnnotSchemeGroup = true;
+ cs = null;
}
else
{
@@ -2466,8 +2988,7 @@ public class Jalview2XML
for (int s = 0; s < groups[i].getSeqCount(); s++)
{
String seqId = groups[i].getSeq(s) + "";
- jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
- .get(seqId);
+ jalview.datamodel.SequenceI ts = seqRefIds.get(seqId);
if (ts != null)
{
@@ -2548,10 +3069,19 @@ 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
@@ -2595,6 +3125,13 @@ 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)
@@ -2622,7 +3159,7 @@ public class Jalview2XML
if (isnewview)
{
- af = loadViewport(file, JSEQ, hiddenSeqs, al, jms, view,
+ af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
uniqueSeqSetId, viewId, autoAlan);
av = af.viewport;
ap = af.alignPanel;
@@ -2707,384 +3244,631 @@ public class Jalview2XML
// //LOAD STRUCTURES
if (loadTreesAndStructures)
{
- // run through all PDB ids on the alignment, and collect mappings between
- // jmol view ids and all sequences referring to it
- Hashtable jmolViewIds = new Hashtable();
+ loadStructures(jprovider, jseqs, af, ap);
+ }
+ // and finally return.
+ return af;
+ }
+
+ /**
+ * Load and link any saved structure viewers.
+ *
+ * @param jprovider
+ * @param jseqs
+ * @param af
+ * @param ap
+ */
+ protected void loadStructures(jarInputStreamProvider jprovider,
+ JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
+ {
+ /*
+ * Run through all PDB ids on the alignment, and collect mappings between
+ * distinct view ids and all sequences referring to that view.
+ */
+ Map structureViewers = new LinkedHashMap();
- for (int i = 0; i < JSEQ.length; i++)
+ for (int i = 0; i < jseqs.length; i++)
+ {
+ if (jseqs[i].getPdbidsCount() > 0)
{
- if (JSEQ[i].getPdbidsCount() > 0)
+ Pdbids[] ids = jseqs[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
{
- Pdbids[] ids = JSEQ[i].getPdbids();
- for (int p = 0; p < ids.length; p++)
+ final int structureStateCount = ids[p].getStructureStateCount();
+ for (int s = 0; s < structureStateCount; s++)
{
- for (int s = 0; s < ids[p].getStructureStateCount(); s++)
+ // check to see if we haven't already created this structure view
+ final StructureState structureState = ids[p]
+ .getStructureState(s);
+ String sviewid = (structureState.getViewId() == null) ? null
+ : structureState.getViewId() + uniqueSetSuffix;
+ jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
+ // Originally : ids[p].getFile()
+ // : TODO: verify external PDB file recovery still works in normal
+ // jalview project load
+ jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ jpdb.setId(ids[p].getId());
+
+ int x = structureState.getXpos();
+ int y = structureState.getYpos();
+ int width = structureState.getWidth();
+ int height = structureState.getHeight();
+
+ // Probably don't need to do this anymore...
+ // Desktop.desktop.getComponentAt(x, y);
+ // TODO: NOW: check that this recovers the PDB file correctly.
+ String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+ jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
+ .getId() + "");
+ if (sviewid == null)
{
- // check to see if we haven't already created this structure view
- String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
- : ids[p].getStructureState(s).getViewId()
- + uniqueSetSuffix;
- jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
- // Originally : ids[p].getFile()
- // : TODO: verify external PDB file recovery still works in normal
- // jalview project load
- jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
- jpdb.setId(ids[p].getId());
-
- int x = ids[p].getStructureState(s).getXpos();
- int y = ids[p].getStructureState(s).getYpos();
- int width = ids[p].getStructureState(s).getWidth();
- int height = ids[p].getStructureState(s).getHeight();
-
- // Probably don't need to do this anymore...
- // Desktop.desktop.getComponentAt(x, y);
- // TODO: NOW: check that this recovers the PDB file correctly.
- String pdbFile = loadPDBFile(jprovider, ids[p].getId());
- jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds
- .get(JSEQ[i].getId() + "");
- if (sviewid == null)
- {
- sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
- + "," + height;
- }
- if (!jmolViewIds.containsKey(sviewid))
- {
- jmolViewIds.put(sviewid, new Object[]
- { new int[]
- { x, y, width, height }, "",
- new Hashtable(), new boolean[]
- { false, false, true } });
- // Legacy pre-2.7 conversion JAL-823 :
- // do not assume any view has to be linked for colour by
- // sequence
- }
+ sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
+ + "," + height;
+ }
+ if (!structureViewers.containsKey(sviewid))
+ {
+ structureViewers.put(sviewid,
+ new StructureViewerModel(x, y, width, height, false,
+ false, true, structureState.getViewId(),
+ structureState.getType()));
+ // Legacy pre-2.7 conversion JAL-823 :
+ // do not assume any view has to be linked for colour by
+ // sequence
+ }
- // assemble String[] { pdb files }, String[] { id for each
- // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
- // seqs_file 2}, boolean[] {
- // linkAlignPanel,superposeWithAlignpanel}} from hash
- Object[] jmoldat = jmolViewIds.get(sviewid);
- ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s)
- .hasAlignwithAlignPanel() ? ids[p].getStructureState(
- s).getAlignwithAlignPanel() : false;
- // never colour by linked panel if not specified
- ((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s)
- .hasColourwithAlignPanel() ? ids[p]
- .getStructureState(s).getColourwithAlignPanel()
- : false;
- // default for pre-2.7 projects is that Jmol colouring is enabled
- ((boolean[]) jmoldat[3])[2] &= ids[p].getStructureState(s)
- .hasColourByJmol() ? ids[p].getStructureState(s)
- .getColourByJmol() : true;
-
- if (((String) jmoldat[1]).length() < ids[p]
- .getStructureState(s).getContent().length())
+ // assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}, boolean[] {
+ // linkAlignPanel,superposeWithAlignpanel}} from hash
+ StructureViewerModel jmoldat = structureViewers.get(sviewid);
+ jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
+ | (structureState.hasAlignwithAlignPanel() ? structureState
+ .getAlignwithAlignPanel() : false));
+
+ /*
+ * Default colour by linked panel to false if not specified (e.g.
+ * for pre-2.7 projects)
+ */
+ boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
+ colourWithAlignPanel |= (structureState
+ .hasColourwithAlignPanel() ? structureState
+ .getColourwithAlignPanel() : false);
+ jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
+
+ /*
+ * Default colour by viewer to true if not specified (e.g. for
+ * pre-2.7 projects)
+ */
+ boolean colourByViewer = jmoldat.isColourByViewer();
+ colourByViewer &= structureState.hasColourByJmol() ? structureState
+ .getColourByJmol() : true;
+ jmoldat.setColourByViewer(colourByViewer);
+
+ if (jmoldat.getStateData().length() < structureState
+ .getContent().length())
+ {
{
- {
- jmoldat[1] = ids[p].getStructureState(s).getContent();
- }
+ jmoldat.setStateData(structureState.getContent());
}
- if (ids[p].getFile() != null)
+ }
+ if (ids[p].getFile() != null)
+ {
+ File mapkey = new File(ids[p].getFile());
+ StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
+ if (seqstrmaps == null)
{
- File mapkey = new File(ids[p].getFile());
- Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
- .get(mapkey);
- if (seqstrmaps == null)
- {
- ((Hashtable) jmoldat[2]).put(mapkey,
- seqstrmaps = new Object[]
- { pdbFile, ids[p].getId(), new Vector(),
- new Vector() });
- }
- if (!((Vector) seqstrmaps[2]).contains(seq))
- {
- ((Vector) seqstrmaps[2]).addElement(seq);
- // ((Vector)seqstrmaps[3]).addElement(n) :
- // in principle, chains
- // should be stored here : do we need to
- // TODO: store and recover seq/pdb_id :
- // chain mappings
- }
+ jmoldat.getFileData().put(
+ mapkey,
+ seqstrmaps = jmoldat.new StructureData(pdbFile,
+ ids[p].getId()));
}
- else
+ if (!seqstrmaps.getSeqList().contains(seq))
{
- errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
- warn(errorMessage);
+ seqstrmaps.getSeqList().add(seq);
+ // TODO and chains?
}
}
+ else
+ {
+ errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
+ warn(errorMessage);
+ }
}
}
}
+ }
+ // Instantiate the associated structure views
+ for (Entry entry : structureViewers
+ .entrySet())
+ {
+ try
+ {
+ createOrLinkStructureViewer(entry, af, ap, jprovider);
+ } catch (Exception e)
+ {
+ System.err.println("Error loading structure viewer: "
+ + e.getMessage());
+ // failed - try the next one
+ }
+ }
+ }
+
+ /**
+ *
+ * @param viewerData
+ * @param af
+ * @param ap
+ * @param jprovider
+ */
+ protected void createOrLinkStructureViewer(
+ Entry viewerData, AlignFrame af,
+ AlignmentPanel ap, jarInputStreamProvider jprovider)
+ {
+ final StructureViewerModel stateData = viewerData.getValue();
+
+ /*
+ * Search for any viewer windows already open from other alignment views
+ * that exactly match the stored structure state
+ */
+ StructureViewerBase comp = findMatchingViewer(viewerData);
+
+ if (comp != null)
+ {
+ linkStructureViewer(ap, comp, stateData);
+ return;
+ }
+
+ /*
+ * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
+ * "viewer_"+stateData.viewId
+ */
+ if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
+ {
+ createChimeraViewer(viewerData, af, jprovider);
+ }
+ else
+ {
+ /*
+ * else Jmol (if pre-2.9, stateData contains JMOL state string)
+ */
+ createJmolViewer(viewerData, af, jprovider);
+ }
+ }
+
+ /**
+ * Create a new Chimera viewer.
+ *
+ * @param data
+ * @param af
+ * @param jprovider
+ */
+ protected void createChimeraViewer(Entry viewerData,
+ AlignFrame af,
+ jarInputStreamProvider jprovider)
+ {
+ StructureViewerModel data = viewerData.getValue();
+ String chimeraSessionFile = data.getStateData();
+
+ /*
+ * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
+ *
+ * Note this is the 'saved' viewId as in the project file XML, _not_ the
+ * 'uniquified' sviewid used to reconstruct the viewer here
+ */
+ chimeraSessionFile = copyJarEntry(jprovider,
+ getViewerJarEntryName(data.getViewId()), "chimera");
+
+ Set> fileData = data.getFileData()
+ .entrySet();
+ List pdbs = new ArrayList();
+ List allseqs = new ArrayList();
+ for (Entry pdb : fileData)
+ {
+ String filePath = pdb.getValue().getFilePath();
+ String pdbId = pdb.getValue().getPdbId();
+ // pdbs.add(new PDBEntry(filePath, pdbId));
+ pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
+ final List seqList = pdb.getValue().getSeqList();
+ SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
+ allseqs.add(seqs);
+ }
+
+ boolean colourByChimera = data.isColourByViewer();
+ boolean colourBySequence = data.isColourWithAlignPanel();
+
+ // TODO use StructureViewer as a factory here, see JAL-1761
+ final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
+ final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
+ .size()][]);
+ String newViewId = viewerData.getKey();
+ ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
+ af.alignPanel, pdbArray,
+ seqsArray, colourByChimera, colourBySequence, newViewId);
+ cvf.setSize(data.getWidth(), data.getHeight());
+ cvf.setLocation(data.getX(), data.getY());
+ }
+
+ /**
+ * Create a new Jmol window. First parse the Jmol state to translate filenames
+ * loaded into the view, and record the order in which files are shown in the
+ * Jmol view, so we can add the sequence mappings in same order.
+ *
+ * @param viewerData
+ * @param af
+ * @param jprovider
+ */
+ protected void createJmolViewer(
+ final Entry viewerData,
+ AlignFrame af, jarInputStreamProvider jprovider)
+ {
+ final StructureViewerModel svattrib = viewerData.getValue();
+ String state = svattrib.getStateData();
+
+ /*
+ * Pre-2.9: state element value is the Jmol state string
+ *
+ * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
+ * + viewId
+ */
+ if (ViewerType.JMOL.toString().equals(svattrib.getType()))
+ {
+ state = readJarEntry(jprovider,
+ getViewerJarEntryName(svattrib.getViewId()));
+ }
+
+ List pdbfilenames = new ArrayList();
+ List seqmaps = new ArrayList();
+ List pdbids = new ArrayList();
+ StringBuilder newFileLoc = new StringBuilder(64);
+ int cp = 0, ncp, ecp;
+ Map oldFiles = svattrib.getFileData();
+ while ((ncp = state.indexOf("load ", cp)) > -1)
+ {
+ 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.
+ StructureData filedat = oldFiles.get(new File(oldfilenam));
+ newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+ pdbfilenames.add(filedat.getFilePath());
+ pdbids.add(filedat.getPdbId());
+ seqmaps.add(filedat.getSeqList().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)
+ {
+ // just append rest of state
+ newFileLoc.append(state.substring(cp));
+ }
+ else
+ {
+ System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
+ newFileLoc = new StringBuilder(state);
+ newFileLoc.append("; load append ");
+ for (File id : oldFiles.keySet())
{
+ // add this and any other pdb files that should be present in
+ // the viewer
+ StructureData filedat = oldFiles.get(id);
+ newFileLoc.append(filedat.getFilePath());
+ pdbfilenames.add(filedat.getFilePath());
+ pdbids.add(filedat.getPdbId());
+ seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
+ newFileLoc.append(" \"");
+ newFileLoc.append(filedat.getFilePath());
+ newFileLoc.append("\"");
+
+ }
+ newFileLoc.append(";");
+ }
- // Instantiate the associated Jmol views
- for (Entry entry : jmolViewIds.entrySet())
+ if (newFileLoc.length() > 0)
+ {
+ int histbug = newFileLoc.indexOf("history = ");
+ histbug += 10;
+ int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
+ String val = (diff == -1) ? null : newFileLoc
+ .substring(histbug, diff);
+ if (val != null && val.length() >= 4)
+ {
+ if (val.contains("e"))
{
- String sviewid = entry.getKey();
- Object[] svattrib = entry.getValue();
- int[] geom = (int[]) svattrib[0];
- String state = (String) svattrib[1];
- Hashtable oldFiles = (Hashtable) svattrib[2];
- final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring = ((boolean[]) svattrib[3])[2];
- int x = geom[0], y = geom[1], width = geom[2], height = geom[3];
- // collate the pdbfile -> sequence mappings from this view
- Vector pdbfilenames = new Vector();
- Vector seqmaps = new Vector();
- Vector pdbids = new Vector();
+ if (val.trim().equals("true"))
+ {
+ val = "1";
+ }
+ else
+ {
+ val = "0";
+ }
+ newFileLoc.replace(histbug, diff, val);
+ }
+ }
- // Search to see if we've already created this Jmol view
- AppJmol comp = null;
- JInternalFrame[] frames = null;
- do
+ final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
+ .size()]);
+ final String[] id = pdbids.toArray(new String[pdbids.size()]);
+ final SequenceI[][] sq = seqmaps
+ .toArray(new SequenceI[seqmaps.size()][]);
+ final String fileloc = newFileLoc.toString();
+ final String sviewid = viewerData.getKey();
+ final AlignFrame alf = af;
+ final Rectangle rect = new Rectangle(svattrib.getX(),
+ svattrib.getY(), svattrib.getWidth(), svattrib.getHeight());
+ try
+ {
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
{
+ JalviewStructureDisplayI sview = null;
try
{
- frames = Desktop.desktop.getAllFrames();
- } catch (ArrayIndexOutOfBoundsException e)
- {
- // occasional No such child exceptions are thrown here...
- frames = null;
- try
- {
- Thread.sleep(10);
- } catch (Exception f)
- {
- }
- ;
- }
- } while (frames == null);
- // search for any Jmol windows already open from other
- // alignment views that exactly match the stored structure state
- for (int f = 0; comp == null && f < frames.length; f++)
- {
- if (frames[f] instanceof AppJmol)
+ sview = new StructureViewer(alf.alignPanel
+ .getStructureSelectionManager()).createView(
+ StructureViewer.ViewerType.JMOL, pdbf, id, sq,
+ alf.alignPanel, svattrib, fileloc, rect, sviewid);
+ addNewStructureViewer(sview);
+ } catch (OutOfMemoryError ex)
{
- if (sviewid != null
- && ((AppJmol) frames[f]).getViewId().equals(sviewid))
- {
- // post jalview 2.4 schema includes structure view id
- comp = (AppJmol) frames[f];
- }
- else if (frames[f].getX() == x && frames[f].getY() == y
- && frames[f].getHeight() == height
- && frames[f].getWidth() == width)
+ new OOMWarning("restoring structure view for PDB id " + id,
+ (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
{
- comp = (AppJmol) frames[f];
+ sview.closeViewer(false);
+ sview.setVisible(false);
+ sview.dispose();
}
}
}
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.", ex);
- if (comp == null)
- {
- // create a new Jmol window.
- // First parse the Jmol state to translate filenames loaded into the
- // view, and record the order in which files are shown in the Jmol
- // view, so we can add the sequence mappings in same order.
- StringBuffer newFileLoc = null;
- int cp = 0, ncp, ecp;
- while ((ncp = state.indexOf("load ", cp)) > -1)
- {
- if (newFileLoc == null)
- {
- newFileLoc = new StringBuffer();
- }
- 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);
- }
- if (cp > 0)
- {
- // just append rest of state
- newFileLoc.append(state.substring(cp));
- }
- else
- {
- System.err
- .print("Ignoring incomplete Jmol state for PDB ids: ");
- newFileLoc = new StringBuffer(state);
- newFileLoc.append("; load append ");
- for (File id : oldFiles.keySet())
- {
- // add this and any other pdb files that should be present in
- // the viewer
- Object[] filedat = oldFiles.get(id);
- String nfilename;
- newFileLoc.append(((String) filedat[0]));
- pdbfilenames.addElement((String) filedat[0]);
- pdbids.addElement((String) filedat[1]);
- seqmaps.addElement(((Vector) filedat[2])
- .toArray(new SequenceI[0]));
- newFileLoc.append(" \"");
- newFileLoc.append((String) filedat[0]);
- newFileLoc.append("\"");
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * Generates a name for the entry in the project jar file to hold state
+ * information for a structure viewer
+ *
+ * @param viewId
+ * @return
+ */
+ protected String getViewerJarEntryName(String viewId)
+ {
+ return "viewer_" + viewId;
+ }
+
+ /**
+ * Returns any open frame that matches given structure viewer data. The match
+ * is based on the unique viewId, or (for older project versions) the frame's
+ * geometry.
+ *
+ * @param viewerData
+ * @return
+ */
+ protected StructureViewerBase findMatchingViewer(
+ Entry viewerData)
+ {
+ final String sviewid = viewerData.getKey();
+ final StructureViewerModel svattrib = viewerData.getValue();
+ StructureViewerBase comp = null;
+ JInternalFrame[] frames = getAllFrames();
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof StructureViewerBase)
+ {
+ /*
+ * Post jalview 2.4 schema includes structure view id
+ */
+ if (sviewid != null
+ && ((StructureViewerBase) frame).getViewId()
+ .equals(sviewid))
+ {
+ comp = (StructureViewerBase) frame;
+ break; // break added in 2.9
+ }
+ /*
+ * Otherwise test for matching position and size of viewer frame
+ */
+ else if (frame.getX() == svattrib.getX()
+ && frame.getY() == svattrib.getY()
+ && frame.getHeight() == svattrib.getHeight()
+ && frame.getWidth() == svattrib.getWidth())
+ {
+ comp = (StructureViewerBase) frame;
+ // no break in faint hope of an exact match on viewId
+ }
+ }
+ }
+ return comp;
+ }
- }
- newFileLoc.append(";");
- }
+ /**
+ * Link an AlignmentPanel to an existing structure viewer.
+ *
+ * @param ap
+ * @param viewer
+ * @param oldFiles
+ * @param useinViewerSuperpos
+ * @param usetoColourbyseq
+ * @param viewerColouring
+ */
+ protected void linkStructureViewer(AlignmentPanel ap,
+ StructureViewerBase viewer, StructureViewerModel stateData)
+ {
+ // NOTE: if the jalview project is part of a shared session then
+ // view synchronization should/could be done here.
- if (newFileLoc != null)
- {
- int histbug = newFileLoc.indexOf("history = ");
- histbug += 10;
- int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";",
- histbug);
- String val = (diff == -1) ? null : newFileLoc.substring(
- histbug, diff);
- if (val != null && val.length() >= 4)
- {
- if (val.contains("e"))
- {
- if (val.trim().equals("true"))
- {
- val = "1";
- }
- else
- {
- val = "0";
- }
- newFileLoc.replace(histbug, diff, val);
- }
- }
- // TODO: assemble String[] { pdb files }, String[] { id for each
- // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
- // seqs_file 2}} from hash
- final String[] pdbf = pdbfilenames
- .toArray(new String[pdbfilenames.size()]), id = pdbids
- .toArray(new String[pdbids.size()]);
- final SequenceI[][] sq = seqmaps
- .toArray(new SequenceI[seqmaps.size()][]);
- final String fileloc = newFileLoc.toString(), vid = sviewid;
- final AlignFrame alf = af;
- final java.awt.Rectangle rect = new java.awt.Rectangle(x, y,
- width, height);
- try
- {
- javax.swing.SwingUtilities.invokeAndWait(new Runnable()
- {
- @Override
- public void run()
- {
- AppJmol sview = null;
- try
- {
- 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 "
- + id, (OutOfMemoryError) ex.getCause());
- if (sview != null && sview.isVisible())
- {
- sview.closeViewer();
- sview.setVisible(false);
- sview.dispose();
- }
- }
- }
- });
- } catch (InvocationTargetException ex)
- {
- warn("Unexpected error when opening Jmol view.", ex);
+ final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
+ final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
+ final boolean viewerColouring = stateData.isColourByViewer();
+ Map oldFiles = stateData.getFileData();
- } catch (InterruptedException e)
- {
- // e.printStackTrace();
- }
- }
+ /*
+ * Add mapping for sequences in this view to an already open viewer
+ */
+ final AAStructureBindingModel binding = viewer.getBinding();
+ for (File id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in the
+ // viewer
+ StructureData filedat = oldFiles.get(id);
+ String pdbFile = filedat.getFilePath();
+ SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
+ binding.getSsm().setMapping(seq, null, pdbFile,
+ jalview.io.AppletFormatAdapter.FILE);
+ binding.addSequenceForStructFile(pdbFile, seq);
+ }
+ // and add the AlignmentPanel's reference to the view panel
+ viewer.addAlignmentPanel(ap);
+ if (useinViewerSuperpos)
+ {
+ viewer.useAlignmentPanelForSuperposition(ap);
+ }
+ else
+ {
+ viewer.excludeAlignmentPanelForSuperposition(ap);
+ }
+ if (usetoColourbyseq)
+ {
+ viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
+ }
+ else
+ {
+ viewer.excludeAlignmentPanelForColourbyseq(ap);
+ }
+ }
- }
- else
- // if (comp != null)
- {
- // NOTE: if the jalview project is part of a shared session then
- // view synchronization should/could be done here.
+ /**
+ * Get all frames within the Desktop.
+ *
+ * @return
+ */
+ protected JInternalFrame[] getAllFrames()
+ {
+ JInternalFrame[] frames = null;
+ // TODO is this necessary - is it safe - risk of hanging?
+ do
+ {
+ try
+ {
+ frames = Desktop.desktop.getAllFrames();
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ // occasional No such child exceptions are thrown here...
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException f)
+ {
+ }
+ }
+ } while (frames == null);
+ return frames;
+ }
- // add mapping for sequences in this view to an already open Jmol
- // instance
- for (File id : oldFiles.keySet())
- {
- // add this and any other pdb files that should be present in the
- // viewer
- Object[] filedat = oldFiles.get(id);
- String pdbFile = (String) filedat[0];
- SequenceI[] seq = ((Vector) filedat[2])
- .toArray(new SequenceI[0]);
- comp.jmb.ssm.setMapping(seq, null, pdbFile,
- jalview.io.AppletFormatAdapter.FILE);
- comp.jmb.addSequenceForStructFile(pdbFile, seq);
- }
- // and add the AlignmentPanel's reference to the Jmol view
- comp.addAlignmentPanel(ap);
- if (useinJmolsuperpos)
- {
- comp.useAlignmentPanelForSuperposition(ap);
- }
- else
- {
- comp.excludeAlignmentPanelForSuperposition(ap);
- }
- if (usetoColourbyseq)
- {
- comp.useAlignmentPanelForColourbyseq(ap, !jmolColouring);
- }
- else
- {
- comp.excludeAlignmentPanelForColourbyseq(ap);
- }
+ /**
+ *
+ * @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;
+ }
}
- // and finally return.
- return af;
+ return true;
}
- Vector newStructureViewers=null;
- protected void addNewStructureViewer(AppJmol sview)
+
+ Vector newStructureViewers = null;
+
+ protected void addNewStructureViewer(JalviewStructureDisplayI sview)
{
- if (newStructureViewers!=null)
+ if (newStructureViewers != null)
{
- sview.jmb.setFinishedLoadingFromArchive(false);
+ sview.getBinding().setFinishedLoadingFromArchive(false);
newStructureViewers.add(sview);
}
}
+
protected void setLoadingFinishedForNewStructureViewers()
{
- if (newStructureViewers!=null)
+ if (newStructureViewers != null)
{
- for (AppJmol sview:newStructureViewers)
+ for (JalviewStructureDisplayI sview : newStructureViewers)
{
- sview.jmb.setFinishedLoadingFromArchive(true);
+ sview.getBinding().setFinishedLoadingFromArchive(true);
}
newStructureViewers.clear();
- newStructureViewers=null;
+ newStructureViewers = null;
}
}
- AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
- Alignment al, JalviewModelSequence jms, Viewport view,
- String uniqueSeqSetId, String viewId,
- ArrayList autoAlan)
+ AlignFrame loadViewport(String file, JSeq[] JSEQ,
+ List hiddenSeqs, Alignment al,
+ JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
+ String viewId, List autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, view.getWidth(), view.getHeight(),
@@ -3098,19 +3882,18 @@ public class Jalview2XML
.getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
}
- af.viewport.gatherViewsHere = view.getGatheredViews();
+ af.viewport.setGatherViewsHere(view.getGatheredViews());
if (view.getSequenceSetId() != null)
{
- jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
- .get(uniqueSeqSetId);
+ AlignmentViewport av = viewportsAdded.get(uniqueSeqSetId);
af.viewport.setSequenceSetId(uniqueSeqSetId);
if (av != null)
{
// propagate shared settings to this new view
- af.viewport.historyList = av.historyList;
- af.viewport.redoList = av.redoList;
+ af.viewport.setHistoryList(av.getHistoryList());
+ af.viewport.setRedoList(av.getRedoList());
}
else
{
@@ -3135,14 +3918,17 @@ public class Jalview2XML
af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
}
- jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
- .size()];
-
- for (int s = 0; s < hiddenSeqs.size(); s++)
- {
- hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
- }
-
+ // jalview.datamodel.SequenceI[] hseqs = new
+ // jalview.datamodel.SequenceI[hiddenSeqs
+ // .size()];
+ //
+ // for (int s = 0; s < hiddenSeqs.size(); s++)
+ // {
+ // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
+ // }
+
+ SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
+ .size()]);
af.viewport.hideSequence(hseqs);
}
@@ -3162,143 +3948,43 @@ public class Jalview2XML
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
- af.viewport.rightAlignIds = view.getRightAlignIds();
- af.viewport.setFont(new java.awt.Font(view.getFontName(), view
- .getFontStyle(), view.getFontSize()));
- af.alignPanel.fontChanged();
+ af.viewport.setRightAlignIds(view.getRightAlignIds());
+ af.viewport.setFont(
+ new java.awt.Font(view.getFontName(), view.getFontStyle(), view
+ .getFontSize()), true);
+ // TODO: allow custom charWidth/Heights to be restored by updating them
+ // after setting font - which means set above to false
af.viewport.setRenderGaps(view.getRenderGaps());
af.viewport.setWrapAlignment(view.getWrapAlignment());
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());
af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
af.viewport.setShowBoxes(view.getShowBoxes());
af.viewport.setShowText(view.getShowText());
- af.viewport.textColour = new java.awt.Color(view.getTextCol1());
- af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
- af.viewport.thresholdTextColour = view.getTextColThreshold();
+ af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
+ af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
+ af.viewport.setThresholdTextColour(view.getTextColThreshold());
af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
.isShowUnconserved() : false);
af.viewport.setStartRes(view.getStartRes());
af.viewport.setStartSeq(view.getStartSeq());
-
+ af.alignPanel.updateLayout();
ColourSchemeI cs = null;
// apply colourschemes
if (view.getBgColour() != null)
{
if (view.getBgColour().startsWith("ucs"))
{
- cs = GetUserColourScheme(jms, view.getBgColour());
+ cs = getUserColourScheme(jms, view.getBgColour());
}
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)
-
- );
- }
-
- if (view.getAnnotationColours().getColourScheme()
- .equals("None"))
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- new java.awt.Color(view.getAnnotationColours()
- .getMinColour()), new java.awt.Color(view
- .getAnnotationColours().getMaxColour()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else if (view.getAnnotationColours().getColourScheme()
- .startsWith("ucs"))
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- GetUserColourScheme(jms, view
- .getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al, view
- .getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold());
- }
- if (view.getAnnotationColours().hasPerSequence())
- {
- ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
- }
- if (view.getAnnotationColours().hasPredefinedColours())
- {
- ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
- }
- // Also use these settings for all the groups
- if (al.getGroups() != null)
- {
- for (int g = 0; g < al.getGroups().size(); g++)
- {
- jalview.datamodel.SequenceGroup sg = al.getGroups()
- .get(g);
-
- if (sg.cs == null)
- {
- continue;
- }
-
- /*
- * if
- * (view.getAnnotationColours().getColourScheme().equals("None"
- * )) { sg.cs = new AnnotationColourGradient(
- * af.viewport.getAlignment().getAlignmentAnnotation()[i], new
- * java.awt.Color(view.getAnnotationColours().
- * getMinColour()), new
- * java.awt.Color(view.getAnnotationColours().
- * getMaxColour()),
- * view.getAnnotationColours().getAboveThreshold()); } else
- */
- {
- sg.cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- sg.cs, view.getAnnotationColours()
- .getAboveThreshold());
- if (cs instanceof AnnotationColourGradient)
- {
- if (view.getAnnotationColours().hasPerSequence())
- {
- ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
- }
- if (view.getAnnotationColours().hasPredefinedColours())
- {
- ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
- }
- }
- }
-
- }
- }
+ AnnotationColours viewAnnColour = view.getAnnotationColours();
+ cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
- break;
- }
+ // annpos
- }
- }
}
else
{
@@ -3324,10 +4010,8 @@ public class Jalview2XML
af.viewport.setColourAppliesToAllGroups(true);
- if (view.getShowSequenceFeatures())
- {
- af.viewport.showSequenceFeatures = true;
- }
+ af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
+
if (view.hasCentreColumnLabels())
{
af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
@@ -3339,7 +4023,7 @@ public class Jalview2XML
}
if (view.hasFollowHighlight())
{
- af.viewport.followHighlight = view.getFollowHighlight();
+ af.viewport.setFollowHighlight(view.getFollowHighlight());
}
if (view.hasFollowSelection())
{
@@ -3368,11 +4052,11 @@ public class Jalview2XML
}
if (view.hasShowDbRefTooltip())
{
- af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
+ af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
}
if (view.hasShowNPfeatureTooltip())
{
- af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
+ af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
}
if (view.hasShowGroupConsensus())
{
@@ -3394,9 +4078,14 @@ public class Jalview2XML
// recover featre settings
if (jms.getFeatureSettings() != null)
{
- af.viewport.featuresDisplayed = new Hashtable();
+ FeaturesDisplayed fdi;
+ af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
+ Hashtable featureGroups = new Hashtable();
+ Hashtable featureColours = new Hashtable();
+ Hashtable featureOrder = new Hashtable();
+
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
@@ -3423,37 +4112,42 @@ public class Jalview2XML
gc.setColourByLabel(setting.getColourByLabel());
}
// and put in the feature colour table.
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
- setting.getType(), gc);
+ featureColours.put(setting.getType(), gc);
}
else
{
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
- setting.getType(),
+ featureColours.put(setting.getType(),
new java.awt.Color(setting.getColour()));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
- setting.getType(), setting.getOrder());
+ {
+ featureOrder.put(setting.getType(), setting.getOrder());
+ }
else
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
- setting.getType(),
- fs / jms.getFeatureSettings().getSettingCount());
+ {
+ featureOrder.put(setting.getType(), new Float(fs
+ / jms.getFeatureSettings().getSettingCount()));
+ }
if (setting.getDisplay())
{
- af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
- setting.getColour()));
+ fdi.setVisible(setting.getType());
}
}
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
- Hashtable fgtable;
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+ Hashtable fgtable = new Hashtable();
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
}
+ // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
+ // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
+ // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
+ FeatureRendererSettings frs = new FeatureRendererSettings(
+ renderOrder, fgtable, featureColours, 1.0f, featureOrder);
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(frs);
+
}
if (view.getHiddenColumnsCount() > 0)
@@ -3483,17 +4177,157 @@ public class Jalview2XML
}
}
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, true); // recompute any autoannotation
- reorderAutoannotation(af, al, autoAlan);
- af.alignPanel.alignmentChanged();
+ /*
+ * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
+ * has a 'cdna/protein complement' view, in which case save it in order to
+ * populate a SplitFrame once all views have been read in.
+ */
+ String complementaryViewId = view.getComplementId();
+ if (complementaryViewId == null)
+ {
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+ view.getHeight());
+ // recompute any autoannotation
+ af.alignPanel.updateAnnotation(false, true);
+ reorderAutoannotation(af, al, autoAlan);
+ af.alignPanel.alignmentChanged();
+ }
+ else
+ {
+ splitFrameCandidates.put(view, af);
+ }
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)
+ List autoAlan)
{
// copy over visualization settings for autocalculated annotation in the
// view
@@ -3517,11 +4351,11 @@ public class Jalview2XML
+ auan.template.getCalcId()), auan);
}
int hSize = al.getAlignmentAnnotation().length;
- ArrayList reorder = new ArrayList();
+ List 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());
+ List remains = new ArrayList(visan.keySet());
for (int h = 0; h < hSize; h++)
{
jalview.datamodel.AlignmentAnnotation jalan = al
@@ -3629,7 +4463,7 @@ public class Jalview2XML
return false;
}
- public void AddToSkipList(AlignFrame af)
+ public void addToSkipList(AlignFrame af)
{
if (skipList == null)
{
@@ -3647,7 +4481,8 @@ public class Jalview2XML
}
}
- private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
+ private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
+ boolean ignoreUnrefed)
{
jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
Vector dseqs = null;
@@ -3659,7 +4494,7 @@ public class Jalview2XML
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
- ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
}
// create a new dataset
if (ds == null)
@@ -3672,7 +4507,7 @@ public class Jalview2XML
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
// set the dataset for the newly imported alignment.
- if (al.getDataset() == null)
+ if (al.getDataset() == null && !ignoreUnrefed)
{
al.setDataset(ds);
}
@@ -3688,25 +4523,27 @@ public class Jalview2XML
* vector to add new dataset sequence to
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
- AlignmentI ds, Vector dseqs)
+ AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
- jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
- .get(vamsasSeq.getId());
- jalview.datamodel.SequenceI dsq = null;
+ SequenceI sq = seqRefIds.get(vamsasSeq.getId());
+ SequenceI dsq = null;
if (sq != null && sq.getDatasetSequence() != null)
{
dsq = sq.getDatasetSequence();
}
-
+ if (sq == null && ignoreUnrefed)
+ {
+ return;
+ }
String sqid = vamsasSeq.getDsseqid();
if (dsq == null)
{
// need to create or add a new dataset sequence reference to this sequence
if (sqid != null)
{
- dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
+ dsq = seqRefIds.get(sqid);
}
// check again
if (dsq == null)
@@ -3737,6 +4574,24 @@ 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);
+ }
+ }
+ }
}
}
}
@@ -3748,7 +4603,7 @@ public class Jalview2XML
// if (pre || post)
if (sq != dsq)
{
- StringBuffer sb = new StringBuffer();
+ // StringBuffer sb = new StringBuffer();
String newres = jalview.analysis.AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, sq.getSequenceAsString());
if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
@@ -3763,11 +4618,12 @@ 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" : ""));
}
@@ -3883,7 +4739,7 @@ public class Jalview2XML
/**
* recover from hash
*/
- jmap.setTo((SequenceI) seqRefIds.get(dsfor));
+ jmap.setTo(seqRefIds.get(dsfor));
}
else
{
@@ -3897,14 +4753,14 @@ public class Jalview2XML
* local sequence definition
*/
Sequence ms = mc.getSequence();
- jalview.datamodel.Sequence djs = null;
+ SequenceI djs = null;
String sqid = ms.getDsseqid();
if (sqid != null && sqid.length() > 0)
{
/*
* recover dataset sequence
*/
- djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
+ djs = seqRefIds.get(sqid);
}
else
{
@@ -3942,7 +4798,7 @@ public class Jalview2XML
boolean keepSeqRefs)
{
initSeqRefs();
- jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
+ jalview.schemabinding.version2.JalviewModel jm = saveState(ap, null,
null);
if (!keepSeqRefs)
@@ -3963,9 +4819,9 @@ public class Jalview2XML
frefedSequence = new Vector();
}
- viewportsAdded = new Hashtable();
+ viewportsAdded.clear();
- AlignFrame af = LoadFromObject(jm, null, false, null);
+ AlignFrame af = loadFromObject(jm, null, false, null);
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
@@ -4099,24 +4955,20 @@ public class Jalview2XML
// register sequence object so the XML parser can recover it.
if (seqRefIds == null)
{
- seqRefIds = new Hashtable();
+ seqRefIds = new HashMap();
}
if (seqsToIds == null)
{
- seqsToIds = new IdentityHashMap();
+ seqsToIds = new IdentityHashMap();
}
- seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
- seqsToIds.put(jvobj, id);
+ seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
+ seqsToIds.put((SequenceI) jvobj, id);
}
else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
{
- if (annotationIds == null)
- {
- annotationIds = new Hashtable();
- }
String anid;
- annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
- jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
+ AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
+ annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvann);
if (jvann.annotationId == null)
{
jvann.annotationId = anid;
@@ -4138,7 +4990,9 @@ public class Jalview2XML
}
}
else
+ {
Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ }
}
}
@@ -4166,4 +5020,66 @@ public class Jalview2XML
skipList = skipList2;
}
+ /**
+ * Reads the jar entry of given name and returns its contents, or null if the
+ * entry is not found.
+ *
+ * @param jprovider
+ * @param jarEntryName
+ * @return
+ */
+ protected String readJarEntry(jarInputStreamProvider jprovider,
+ String jarEntryName)
+ {
+ String result = null;
+ BufferedReader in = null;
+
+ try
+ {
+ /*
+ * Reopen the jar input stream and traverse its entries to find a matching
+ * name
+ */
+ JarInputStream jin = jprovider.getJarInputStream();
+ JarEntry entry = null;
+ do
+ {
+ entry = jin.getNextJarEntry();
+ } while (entry != null && !entry.getName().equals(jarEntryName));
+
+ if (entry != null)
+ {
+ StringBuilder out = new StringBuilder(256);
+ in = new BufferedReader(new InputStreamReader(jin, UTF_8));
+ String data;
+
+ while ((data = in.readLine()) != null)
+ {
+ out.append(data);
+ }
+ result = out.toString();
+ }
+ else
+ {
+ warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+
+ return result;
+ }
}