/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
*
*/
package jalview.gui;
+import java.awt.Rectangle;
+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.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.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.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+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.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
import jalview.schemabinding.version2.AlcodMap;
-import jalview.schemabinding.version2.Alcodon;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.schemabinding.version2.Annotation;
import jalview.schemabinding.version2.AnnotationColours;
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;
import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
-import java.awt.Rectangle;
-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.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map.Entry;
-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.JInternalFrame;
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
-
-import org.exolab.castor.xml.Unmarshaller;
-
/**
* Write out the current jalview desktop state as a Jalview XML stream.
*
*/
public class Jalview2XML
{
+ /*
+ * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
+ * of sequence objects are created.
+ */
+ IdentityHashMap<SequenceI, String> 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<String, SequenceI> 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<Viewport, AlignFrame> splitFrameCandidates = new HashMap<Viewport, AlignFrame>();
+
/**
* create/return unique hash string for sq
*
}
if (seqsToIds.containsKey(sq))
{
- return (String) seqsToIds.get(sq);
+ return seqsToIds.get(sq);
}
else
{
{
if (seqsToIds == null)
{
- seqsToIds = new IdentityHashMap();
+ seqsToIds = new IdentityHashMap<SequenceI, String>();
}
if (seqRefIds == null)
{
- seqRefIds = new Hashtable();
+ seqRefIds = new HashMap<String, SequenceI>();
}
}
- /**
- * 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()
{
}
{
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();
{
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();
}
/**
- * 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<String, AlignViewport> viewportsAdded = new HashMap<String, AlignViewport>();
- Hashtable annotationIds = new Hashtable();
+ Map<String, AlignmentAnnotation> annotationIds = new HashMap<String, AlignmentAnnotation>();
String uniqueSetSuffix = "";
/**
* List of pdbfiles added to Jar
*/
- Vector pdbfiles = null;
+ List<String> 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)
{
errorMessage += "(output file was '" + statefile + "')";
}
e.printStackTrace();
+ } finally
+ {
+ if (fos != null)
+ {
+ try
+ {
+ fos.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
}
reportErrors();
}
*
* @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)
{
// 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();
// 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;
- }
+ continue;
+ }
+
+ String shortName = af.getTitle();
+
+ if (shortName.indexOf(File.separatorChar) > -1)
+ {
+ shortName = shortName.substring(shortName
+ .lastIndexOf(File.separatorChar) + 1);
+ }
- String shortName = af.getTitle();
+ int count = 1;
- if (shortName.indexOf(File.separatorChar) > -1)
+ while (shortNames.contains(shortName))
+ {
+ if (shortName.endsWith("_" + (count - 1)))
{
- shortName = shortName.substring(shortName
- .lastIndexOf(File.separatorChar) + 1);
+ shortName = shortName.substring(0, shortName.lastIndexOf("_"));
}
- int count = 1;
+ shortName = shortName.concat("_" + count);
+ count++;
+ }
- while (shortNames.contains(shortName))
- {
- if (shortName.endsWith("_" + (count - 1)))
- {
- shortName = shortName
- .substring(0, shortName.lastIndexOf("_"));
- }
+ shortNames.addElement(shortName);
- shortName = shortName.concat("_" + count);
- count++;
- }
+ if (!shortName.endsWith(".xml"))
+ {
+ shortName = shortName + ".xml";
+ }
- shortNames.addElement(shortName);
+ int ap, apSize = af.alignPanels.size();
- if (!shortName.endsWith(".xml"))
+ for (ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = af.alignPanels.get(ap);
+ String fileName = apSize == 1 ? shortName : ap + shortName;
+ if (!fileName.endsWith(".xml"))
{
- shortName = shortName + ".xml";
+ fileName = fileName + ".xml";
}
- int ap, apSize = af.alignPanels.size();
+ saveState(apanel, fileName, jout);
- for (ap = 0; ap < apSize; ap++)
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
+ if (!dsses.containsKey(dssid))
{
- 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);
-
- String dssid = getDatasetIdRef(af.getViewport().getAlignment()
- .getDataset());
- if (!dsses.containsKey(dssid))
- {
- dsses.put(dssid, af);
- }
-
+ dsses.put(dssid, af);
}
}
}
}
// 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);
Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
- for (ap = 0; ap < apSize; ap++)
+ 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))
{
jfileName = jfileName + ".xml";
}
- SaveState(_af.alignPanel, jfileName, true, jout);
+ 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
* @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);
+ return saveState(ap, fileName, false, 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
* @param out
* jar entry name
*/
- public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+ public JalviewModel saveState(AlignmentPanel ap, String fileName,
boolean storeDS, JarOutputStream jout)
{
initSeqRefs();
- Vector jmolViewIds = new Vector(); //
- Vector userColours = new Vector();
+ List<String> viewIds = new ArrayList<String>();
+ List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
AlignViewport av = ap.av;
}
}
- if (jdatasq.getSequenceFeatures() != null)
+ if (jds.getSequenceFeatures() != null)
{
- jalview.datamodel.SequenceFeature[] sf = jdatasq
+ jalview.datamodel.SequenceFeature[] sf = jds
.getSequenceFeatures();
int index = 0;
while (index < sf.length)
pdb.setId(entry.getId());
pdb.setType(entry.getType());
- //
- // store any JMol views associated with this seqeunce
- // this section copes with duplicate entries in the project, so a
- // dataset only view *should* be coped with sensibly
- AppJmol jmol;
+
+ /*
+ * 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++)
- {
- 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)
- {
- matchedFile = jmol.jmb.pdbentry[peid].getFile();
- }
- else if (!matchedFile.equals(jmol.jmb.pdbentry[peid]
- .getFile()))
- {
- 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);
- }
-
- }
- }
+ StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
+ matchedFile = saveStructureState(ap, jds, pdb, entry,
+ viewIds, matchedFile, viewFrame);
}
}
pdb.setFile(matchedFile); // entry.getFile());
if (pdbfiles == null)
{
- pdbfiles = new Vector();
+ pdbfiles = new ArrayList<String>();
}
if (!pdbfiles.contains(entry.getId()))
{
- pdbfiles.addElement(entry.getId());
+ pdbfiles.add(entry.getId());
+ DataInputStream dis = null;
try
{
File file = new File(matchedFile);
{
byte[] data = new byte[(int) file.length()];
jout.putNextEntry(new JarEntry(entry.getId()));
- DataInputStream dis = new DataInputStream(
- new FileInputStream(file));
+ dis = new DataInputStream(new FileInputStream(file));
dis.readFully(data);
DataOutputStream dout = new DataOutputStream(jout);
} catch (Exception ex)
{
ex.printStackTrace();
+ } finally
+ {
+ if (dis != null)
+ {
+ try
+ {
+ dis.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
}
}
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<AlignedCodonFrame> 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();
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);
+// }
+// }
}
}
if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
- groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+ groups[i].setColour(setUserColourScheme(sg.cs, userColours,
jms));
}
else
else if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
groups[i]
- .setColour(SetUserColourScheme(sg.cs, userColours, jms));
+ .setColour(setUserColourScheme(sg.cs, userColours, jms));
}
else
{
view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
av.getSequenceSetId()));
view.setId(av.getViewId());
- view.setViewName(av.viewName);
- view.setGatheredViews(av.gatherViewsHere);
-
- if (ap.av.explodedPosition != null)
+ if (av.getCodingComplement() != null)
{
- view.setXpos(av.explodedPosition.x);
- view.setYpos(av.explodedPosition.y);
- view.setWidth(av.explodedPosition.width);
- view.setHeight(av.explodedPosition.height);
+ view.setComplementId(av.getCodingComplement().getViewId());
}
- else
+ view.setViewName(av.viewName);
+ view.setGatheredViews(av.isGatherViewsHere());
+
+ Rectangle position = ap.av.getExplodedGeometry();
+ if (position == null)
{
- view.setXpos(ap.alignFrame.getBounds().x);
- view.setYpos(ap.alignFrame.getBounds().y);
- view.setWidth(ap.alignFrame.getBounds().width);
- view.setHeight(ap.alignFrame.getBounds().height);
+ position = ap.alignFrame.getBounds();
}
+ view.setXpos(position.x);
+ view.setYpos(position.y);
+ view.setWidth(position.width);
+ view.setHeight(position.height);
view.setStartRes(av.startRes);
view.setStartSeq(av.startSeq);
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
- view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
+ view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
userColours, jms));
}
else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
view.setConsThreshold(cs.getConservationInc());
if (cs instanceof jalview.schemes.UserColourScheme)
{
- view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+ view.setBgColour(setUserColourScheme(cs, userColours, jms));
}
}
view.setFontName(av.font.getName());
view.setFontSize(av.font.getSize());
view.setFontStyle(av.font.getStyle());
- view.setRenderGaps(av.renderGaps);
- view.setShowAnnotation(av.getShowAnnotation());
+ view.setRenderGaps(av.isRenderGaps());
+ view.setShowAnnotation(av.isShowAnnotation());
view.setShowBoxes(av.getShowBoxes());
view.setShowColourText(av.getColourText());
view.setShowFullId(av.getShowJVSuffix());
- view.setRightAlignIds(av.rightAlignIds);
- view.setShowSequenceFeatures(av.showSequenceFeatures);
+ view.setRightAlignIds(av.isRightAlignIds());
+ view.setShowSequenceFeatures(av.isShowSequenceFeatures());
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.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.setShowNPfeatureTooltip(av.isShowNPFeats());
+ view.setShowDbRefTooltip(av.isShowDBRefs());
view.setFollowHighlight(av.followHighlight);
view.setFollowSelection(av.followSelection);
- view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
- if (av.featuresDisplayed != null)
+ view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
+ if (av.getFeaturesDisplayed() != null)
{
jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+ String[] renderOrder = ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer().getRenderOrder()
+ .toArray(new String[0]);
Vector settingsAdded = new Vector();
Object gstyle = null;
{
for (int ro = 0; ro < renderOrder.length; ro++)
{
- gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getFeatureStyle(renderOrder[ro]);
Setting setting = new Setting();
setting.setType(renderOrder[ro]);
}
else
{
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ setting.setColour(ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer()
.getColour(renderOrder[ro]).getRGB());
}
- setting.setDisplay(av.featuresDisplayed
- .containsKey(renderOrder[ro]));
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ setting.setDisplay(av.getFeaturesDisplayed().isVisible(
+ renderOrder[ro]));
+ float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getOrder(renderOrder[ro]);
if (rorder > -1)
{
}
// Make sure we save none displayed feature settings
- Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
- .keySet().iterator();
+ Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getFeatureColours().keySet().iterator();
while (en.hasNext())
{
String key = en.next().toString();
Setting setting = new Setting();
setting.setType(key);
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getColour(key).getRGB());
setting.setDisplay(false);
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getOrder(key);
if (rorder > -1)
{
fs.addSetting(setting);
settingsAdded.addElement(key);
}
- en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
- .keySet().iterator();
+ // is groups actually supposed to be a map here ?
+ en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getFeatureGroups().iterator();
Vector groupsAdded = new Vector();
while (en.hasNext())
{
}
Group g = new Group();
g.setName(grp);
- g.setDisplay(((Boolean) ap.seqPanel.seqCanvas
- .getFeatureRenderer().featureGroups.get(grp))
+ g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer().checkGroupVisibility(grp, false))
.booleanValue());
fs.addGroup(g);
groupsAdded.addElement(grp);
for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
.size(); c++)
{
- int[] region = (int[]) av.getColumnSelection()
- .getHiddenColumns().elementAt(c);
+ int[] region = av.getColumnSelection().getHiddenColumns()
+ .get(c);
HiddenColumns hc = new HiddenColumns();
hc.setStart(region[0]);
hc.setEnd(region[1]);
return object;
}
+ /**
+ * 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<String> viewIds,
+ String matchedFile, StructureViewerBase viewFrame)
+ {
+ final AAStructureBindingModel bindingModel = viewFrame.getBinding();
+ 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())))
+ {
+ 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)
+ String statestring = viewFrame.getStateInfo();
+
+ 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());
+ /*
+ * Only store each structure viewer's state once in each XML document.
+ */
+ if (!viewIds.contains(viewId))
+ {
+ viewIds.add(viewId);
+ state.setContent(statestring.replaceAll("\n", ""));
+ }
+ else
+ {
+ state.setContent("# duplicate state");
+ }
+ pdb.addStructureState(state);
+ }
+ }
+ }
+ return matchedFile;
+ }
+
private AnnotationColours constructAnnotationColours(
- AnnotationColourGradient acg, Vector userColours,
+ AnnotationColourGradient acg, List<UserColourScheme> userColours,
JalviewModelSequence jms)
{
AnnotationColours ac = new AnnotationColours();
ac.setAnnotation(acg.getAnnotation());
if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
{
- ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+ ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
userColours, jms));
}
else
an.addProperty(prop);
}
}
+
AnnotationElement ae;
if (aa[i].annotations != null)
{
return false;
}
}
- throw new Error(MessageManager.formatMessage("error.unsupported_version_calcIdparam", new String[]{calcIdParam.toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.unsupported_version_calcIdparam", new Object[]
+ { calcIdParam.toString() }));
}
/**
mp = new Mapping();
jalview.util.MapList mlst = jmp.getMap();
- int r[] = mlst.getFromRanges();
- for (int s = 0; s < r.length; s += 2)
+ List<int[]> 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());
return mp;
}
- String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
- Vector userColours, JalviewModelSequence jms)
+ String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
+ List<UserColourScheme> userColours, JalviewModelSequence jms)
{
String id = null;
jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
return id;
}
- jalview.schemes.UserColourScheme GetUserColourScheme(
+ jalview.schemes.UserColourScheme getUserColourScheme(
JalviewModelSequence jms, String id)
{
UserColours[] uc = jms.getUserColours();
* @param file
* - HTTP URL or filename
*/
- public AlignFrame LoadJalviewAlign(final String file)
+ public AlignFrame loadJalviewAlign(final String file)
{
jalview.gui.AlignFrame af = null;
// 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 = null;
uniqueSetSuffix = null;
seqRefIds = null;
- viewportsAdded = null;
+ viewportsAdded.clear();
frefedSequence = null;
if (file.startsWith("http://"))
* @param jprovider
* @return
*/
- public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
+ public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
{
errorMessage = null;
if (uniqueSetSuffix == null)
}
if (seqRefIds == null)
{
- seqRefIds = new Hashtable();
- }
- if (viewportsAdded == null)
- {
- viewportsAdded = new Hashtable();
+ seqRefIds = new HashMap<String, SequenceI>();
}
if (frefedSequence == null)
{
frefedSequence = new Vector();
}
- jalview.gui.AlignFrame af = null, _af = null;
- Hashtable gatherToThisFrame = new Hashtable();
+ AlignFrame af = null, _af = null;
+ Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
final String file = jprovider.getFilename();
try
{
object = (JalviewModel) unmar.unmarshal(in);
if (true) // !skipViewport(object))
{
- _af = LoadFromObject(object, file, true, jprovider);
+ _af = loadFromObject(object, file, true, jprovider);
if (object.getJalviewModelSequence().getViewportCount() > 0)
{
af = _af;
- if (af.viewport.gatherViewsHere)
+ if (af.viewport.isGatherViewsHere())
{
gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
}
Desktop.instance.stopLoading();
}
- Enumeration en = gatherToThisFrame.elements();
- while (en.hasMoreElements())
+ /*
+ * 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((AlignFrame) en.nextElement());
+ Desktop.instance.gatherViews(fr);
}
+
+ restoreSplitFrames();
+
if (errorMessage != null)
{
reportErrors();
}
/**
+ * 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<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
+ List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
+ Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
+
+ /*
+ * Identify the DNA alignments
+ */
+ for (Entry<Viewport, AlignFrame> 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<Viewport, AlignFrame> 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<Viewport, AlignFrame> 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;
+ }
+
+ /**
* check errorMessage for a valid error message and raise an error box in the
* GUI or write the current errorMessage to stderr and then clear the error
* state.
errorMessage = null;
}
- Hashtable<String, String> alreadyLoadedPDB;
+ Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
/**
* when set, local views will be updated from view stored in JalviewXML
String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
{
- if (alreadyLoadedPDB == null)
- {
- alreadyLoadedPDB = new Hashtable();
- }
-
if (alreadyLoadedPDB.containsKey(pdbId))
{
return alreadyLoadedPDB.get(pdbId).toString();
* 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);
// ////////////////////////////////
// LOAD SEQUENCES
- Vector hiddenSeqs = null;
+ List<SequenceI> hiddenSeqs = null;
jalview.datamodel.Sequence jseq;
- ArrayList tmpseqs = new ArrayList();
+ List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
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)
{
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<SequenceI>();
}
- hiddenSeqs.addElement(seqRefIds.get(seqId));
+ hiddenSeqs.add(seqRefIds.get(seqId));
}
}
// /
// 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++)
}
// ///////////////////////////////
- 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(
{
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();
}
}
StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance)
- .registerPDBEntry(entry);
+ Desktop.instance).registerPDBEntry(entry);
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
}
}
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.
}
al.addCodonFrame(cf);
}
-
}
// ////////////////////////////////
// LOAD ANNOTATIONS
- ArrayList<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
+ List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
/**
* store any annotations which forward reference a group's ID
*/
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())
{
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)
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)
{
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;
// //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<String, Object[]> jmolViewIds = new Hashtable();
+ loadStructures(jprovider, jseqs, af, ap);
+ }
+ // and finally return.
+ return af;
+ }
- for (int i = 0; i < JSEQ.length; i++)
+ /**
+ * 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<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
+
+ 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<String, Object[]>(), 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));
+ // 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<String, StructureViewerModel> entry : structureViewers
+ .entrySet())
+ {
+ createOrLinkStructureViewer(entry, af, ap);
+ }
+ }
+
+ /**
+ *
+ * @param viewerData
+ * @param af
+ * @param ap
+ */
+ protected void createOrLinkStructureViewer(
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af,
+ AlignmentPanel ap)
+ {
+ final StructureViewerModel svattrib = 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, svattrib);
+ return;
+ }
+
+ /*
+ * Pending an XML element for ViewerType, just check if stateData contains
+ * "chimera" (part of the chimera session filename).
+ */
+ if (svattrib.getStateData().indexOf("chimera") > -1)
+ {
+ createChimeraViewer(viewerData, af);
+ }
+ else
+ {
+ createJmolViewer(viewerData, af);
+ }
+ }
+
+ /**
+ * Create a new Chimera viewer.
+ *
+ * @param viewerData
+ * @param af
+ */
+ protected void createChimeraViewer(
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af)
+ {
+ final StructureViewerModel data = viewerData.getValue();
+ String chimeraSession = data.getStateData();
+
+ if (new File(chimeraSession).exists())
+ {
+ Set<Entry<File, StructureData>> fileData = data.getFileData()
+ .entrySet();
+ List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
+ List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
+ for (Entry<File, StructureData> pdb : fileData)
+ {
+ String filePath = pdb.getValue().getFilePath();
+ String pdbId = pdb.getValue().getPdbId();
+ pdbs.add(new PDBEntry(filePath, pdbId));
+ final List<SequenceI> seqList = pdb.getValue().getSeqList();
+ SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
+ allseqs.add(seqs);
+ }
+
+ boolean colourByChimera = data.isColourByViewer();
+ boolean colourBySequence = data.isColourWithAlignPanel();
+
+ // TODO can/should this be done via StructureViewer (like Jmol)?
+ final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
+ final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
+ .size()][]);
+ new ChimeraViewFrame(chimeraSession, af.alignPanel, pdbArray,
+ seqsArray, colourByChimera, colourBySequence);
+ }
+ else
+ {
+ Cache.log.error("Chimera session file " + chimeraSession
+ + " not found");
+ }
+ }
+
+ /**
+ * 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
+ */
+ protected void createJmolViewer(
+ final Entry<String, StructureViewerModel> viewerData,
+ AlignFrame af)
+ {
+ final StructureViewerModel svattrib = viewerData.getValue();
+ String state = svattrib.getStateData();
+ List<String> pdbfilenames = new ArrayList<String>();
+ List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
+ List<String> pdbids = new ArrayList<String>();
+ StringBuilder newFileLoc = new StringBuilder(64);
+ int cp = 0, ncp, ecp;
+ Map<File, StructureData> 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<String, Object[]> 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<File, Object[]> oldFiles = (Hashtable<File, Object[]>) 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<String> pdbfilenames = new Vector<String>();
- Vector<SequenceI[]> seqmaps = new Vector<SequenceI[]>();
- Vector<String> pdbids = new Vector<String>();
-
- // Search to see if we've already created this Jmol view
- AppJmol comp = null;
- JInternalFrame[] frames = null;
- do
+ if (val.trim().equals("true"))
{
- 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++)
+ val = "1";
+ }
+ else
{
- if (frames[f] instanceof AppJmol)
- {
- 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)
- {
- comp = (AppJmol) frames[f];
- }
- }
+ val = "0";
}
+ newFileLoc.replace(histbug, diff, val);
+ }
+ }
- if (comp == null)
+ 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()
{
- // 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<SequenceI>) 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)
+ JalviewStructureDisplayI sview = null;
+ try
{
- // just append rest of state
- newFileLoc.append(state.substring(cp));
- }
- else
+ // JAL-1333 note - we probably can't migrate Jmol views to UCSF
+ // Chimera!
+ sview = new StructureViewer(alf.alignPanel
+ .getStructureSelectionManager()).createView(
+ StructureViewer.ViewerType.JMOL, pdbf, id, sq,
+ alf.alignPanel, svattrib, fileloc, rect, sviewid);
+ addNewStructureViewer(sview);
+ } catch (OutOfMemoryError ex)
{
- System.err
- .print("Ignoring incomplete Jmol state for PDB ids: ");
- newFileLoc = new StringBuffer(state);
- newFileLoc.append("; load append ");
- for (File id : oldFiles.keySet())
+ new OOMWarning("restoring structure view for PDB id " + id,
+ (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
{
- // 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<SequenceI>) filedat[2])
- .toArray(new SequenceI[0]));
- newFileLoc.append(" \"");
- newFileLoc.append((String) filedat[0]);
- newFileLoc.append("\"");
-
+ sview.closeViewer(false);
+ sview.setVisible(false);
+ sview.dispose();
}
- newFileLoc.append(";");
}
+ }
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.", ex);
- 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()
- {
- JalviewStructureDisplayI sview = null;
- try
- {
- // JAL-1333 note - we probably can't migrate Jmol views to UCSF Chimera!
- sview = new StructureViewer(alf.alignPanel.getStructureSelectionManager()).createView(StructureViewer.Viewer.JMOL, 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);
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
+ }
+ }
- } catch (InterruptedException e)
- {
- // e.printStackTrace();
- }
- }
+ /**
+ * 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<String, StructureViewerModel> 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 = (AppJmol) frame;
+ // todo: break?
+ }
+ /*
+ * 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 = (AppJmol) frame;
+ // todo: break?
+ }
+ }
+ }
+ return comp;
+ }
- }
- else
- // if (comp != null)
- {
- // NOTE: if the jalview project is part of a shared session then
- // view synchronization should/could be done here.
+ /**
+ * 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 svattrib)
+ {
+ // NOTE: if the jalview project is part of a shared session then
+ // view synchronization should/could be done here.
- // 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<SequenceI>) 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);
- }
- }
+ final boolean useinViewerSuperpos = svattrib.isAlignWithPanel();
+ final boolean usetoColourbyseq = svattrib.isColourWithAlignPanel();
+ final boolean viewerColouring = svattrib.isColourByViewer();
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
+
+ /*
+ * 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);
+ }
+ }
+
+ /**
+ * 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)
+ {
}
}
- }
- // and finally return.
- return af;
+ } while (frames == null);
+ return frames;
}
/**
}
}
- AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
- Alignment al, JalviewModelSequence jms, Viewport view,
- String uniqueSeqSetId, String viewId,
- ArrayList<JvAnnotRow> autoAlan)
+ AlignFrame loadViewport(String file, JSeq[] JSEQ,
+ List<SequenceI> hiddenSeqs, Alignment al,
+ JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
+ String viewId, List<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, view.getWidth(), view.getHeight(),
.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
{
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);
}
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"))
{
af.viewport.setColourAppliesToAllGroups(true);
- if (view.getShowSequenceFeatures())
- {
- af.viewport.showSequenceFeatures = true;
- }
+ af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
+
if (view.hasCentreColumnLabels())
{
af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
}
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())
{
// 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);
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)
}
}
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;
}
{
cs = new AnnotationColourGradient(
annAlignment.getAlignmentAnnotation()[i],
- GetUserColourScheme(jms,
+ getUserColourScheme(jms,
viewAnnColour.getColourScheme()),
viewAnnColour.getAboveThreshold());
}
}
private void reorderAutoannotation(AlignFrame af, Alignment al,
- ArrayList<JvAnnotRow> autoAlan)
+ List<JvAnnotRow> autoAlan)
{
// copy over visualization settings for autocalculated annotation in the
// view
+ auan.template.getCalcId()), auan);
}
int hSize = al.getAlignmentAnnotation().length;
- ArrayList<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+ List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
// 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<String> remains = new ArrayList(visan.keySet());
+ List<String> remains = new ArrayList<String>(visan.keySet());
for (int h = 0; h < hSize; h++)
{
jalview.datamodel.AlignmentAnnotation jalan = al
return false;
}
- public void AddToSkipList(AlignFrame af)
+ public void addToSkipList(AlignFrame af)
{
if (skipList == null)
{
{
// 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();
// 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)
// 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())
/**
* recover from hash
*/
- jmap.setTo((SequenceI) seqRefIds.get(dsfor));
+ jmap.setTo(seqRefIds.get(dsfor));
}
else
{
* 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
{
boolean keepSeqRefs)
{
initSeqRefs();
- jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
+ jalview.schemabinding.version2.JalviewModel jm = saveState(ap, null,
null);
if (!keepSeqRefs)
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);
// register sequence object so the XML parser can recover it.
if (seqRefIds == null)
{
- seqRefIds = new Hashtable();
+ seqRefIds = new HashMap<String, SequenceI>();
}
if (seqsToIds == null)
{
- seqsToIds = new IdentityHashMap();
+ seqsToIds = new IdentityHashMap<SequenceI, String>();
}
- 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;
{
skipList = skipList2;
}
-
}
git://source.jalview.org / jalview.git / blobdiff