X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=e88b190a79833cc354bbde21e6f1dd3114df8b14;hb=8f2bef6f91e7a6e47e41e78a82f45f7e406ef90a;hp=b6e60410ad70ca7ab9688f52058165e271da50c7;hpb=c3184ec60d0f185c89d50d8be0ec9dfc9b26c524;p=jalview.git
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
old mode 100755
new mode 100644
index b6e6041..e88b190
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,50 +1,229 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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 .
*/
package jalview.gui;
+import java.awt.Rectangle;
import java.io.*;
+import java.lang.reflect.InvocationTargetException;
import java.net.*;
import java.util.*;
+import java.util.Map.Entry;
import java.util.jar.*;
import javax.swing.*;
import org.exolab.castor.xml.*;
+
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
import jalview.schemes.*;
-import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
+import jalview.util.jarInputStreamProvider;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.dm.AAConSettings;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.AutoCalcSetting;
+import jalview.ws.params.WsParamSetI;
/**
- * DOCUMENT ME!
- *
+ * Write out the current jalview desktop state as a Jalview XML stream.
+ *
+ * Note: the vamsas objects referred to here are primitive versions of the
+ * VAMSAS project schema elements - they are not the same and most likely never
+ * will be :)
+ *
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.134 $
*/
public class Jalview2XML
{
+ /**
+ * create/return unique hash string for sq
+ *
+ * @param sq
+ * @return new or existing unique string for sq
+ */
+ String seqHash(SequenceI sq)
+ {
+ if (seqsToIds == null)
+ {
+ initSeqRefs();
+ }
+ if (seqsToIds.containsKey(sq))
+ {
+ return (String) seqsToIds.get(sq);
+ }
+ else
+ {
+ // create sequential key
+ String key = "sq" + (seqsToIds.size() + 1);
+ key = makeHashCode(sq, key); // check we don't have an external reference
+ // for it already.
+ seqsToIds.put(sq, key);
+ return key;
+ }
+ }
+
+ void clearSeqRefs()
+ {
+ if (_cleartables)
+ {
+ if (seqRefIds != null)
+ {
+ seqRefIds.clear();
+ }
+ if (seqsToIds != null)
+ {
+ seqsToIds.clear();
+ }
+ // seqRefIds = null;
+ // seqsToIds = null;
+ }
+ else
+ {
+ // do nothing
+ warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
+ // seqRefIds = new Hashtable();
+ // seqsToIds = new IdentityHashMap();
+ }
+ }
+
+ void initSeqRefs()
+ {
+ if (seqsToIds == null)
+ {
+ seqsToIds = new IdentityHashMap();
+ }
+ if (seqRefIds == null)
+ {
+ seqRefIds = new Hashtable();
+ }
+ }
+
+ /**
+ * 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;
- Hashtable seqRefIds;
+ boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+
+ public Jalview2XML()
+ {
+ }
+
+ public Jalview2XML(boolean raiseGUI)
+ {
+ this.raiseGUI = raiseGUI;
+ }
+
+ public void resolveFrefedSequences()
+ {
+ if (frefedSequence.size() > 0)
+ {
+ int r = 0, rSize = frefedSequence.size();
+ while (r < rSize)
+ {
+ Object[] ref = (Object[]) frefedSequence.elementAt(r);
+ if (ref != null)
+ {
+ String sref = (String) ref[0];
+ if (seqRefIds.containsKey(sref))
+ {
+ if (ref[1] instanceof jalview.datamodel.Mapping)
+ {
+ SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
+ }
+ else
+ {
+ if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
+ {
+ SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ if (ref[2] != null
+ && ref[2] instanceof jalview.datamodel.Mapping)
+ {
+ jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
+ ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
+ seq, mp.getTo(), mp.getMap());
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
+ + ref[2].getClass() + " type objects.");
+ }
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
+ + ref[1].getClass() + " type objects.");
+ }
+ }
+ frefedSequence.remove(r);
+ rSize--;
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
+ + ref[0]
+ + " with objecttype "
+ + ref[1].getClass());
+ r++;
+ }
+ }
+ else
+ {
+ // empty reference
+ frefedSequence.remove(r);
+ rSize--;
+ }
+ }
+ }
+ }
/**
- * This maintains a list of viewports, the key being the
- * seqSetId. Important to set historyItem and redoList
- * for multiple views
+ * This maintains a list of viewports, the key being the seqSetId. Important
+ * to set historyItem and redoList for multiple views
*/
Hashtable viewportsAdded;
@@ -52,9 +231,45 @@ public class Jalview2XML
String uniqueSetSuffix = "";
+ /**
+ * List of pdbfiles added to Jar
+ */
+ Vector pdbfiles = null;
+
// SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
public void SaveState(File statefile)
{
+ try
+ {
+ FileOutputStream fos = new FileOutputStream(statefile);
+ JarOutputStream jout = new JarOutputStream(fos);
+ SaveState(jout);
+
+ } catch (Exception e)
+ {
+ // TODO: inform user of the problem - they need to know if their data was
+ // not saved !
+ if (errorMessage == null)
+ {
+ errorMessage = "Couldn't write Jalview Archive to output file '"
+ + statefile + "' - See console error log for details";
+ }
+ else
+ {
+ errorMessage += "(output file was '" + statefile + "')";
+ }
+ e.printStackTrace();
+ }
+ reportErrors();
+ }
+
+ /**
+ * Writes a jalview project archive to the given Jar output stream.
+ *
+ * @param jout
+ */
+ public void SaveState(JarOutputStream jout)
+ {
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
if (frames == null)
@@ -64,29 +279,34 @@ public class Jalview2XML
try
{
- FileOutputStream fos = new FileOutputStream(statefile);
- JarOutputStream jout = new JarOutputStream(fos);
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
- ////////////////////////////////////////////////////
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
+ // 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
+ // REVERSE ORDER
for (int i = frames.length - 1; i > -1; i--)
{
if (frames[i] instanceof AlignFrame)
{
AlignFrame af = (AlignFrame) frames[i];
+ // skip ?
+ if (skipList != null
+ && skipList.containsKey(af.getViewport()
+ .getSequenceSetId()))
+ {
+ continue;
+ }
String shortName = af.getTitle();
if (shortName.indexOf(File.separatorChar) > -1)
{
- shortName = shortName.substring(shortName.lastIndexOf(
- File.separatorChar) + 1);
+ shortName = shortName.substring(shortName
+ .lastIndexOf(File.separatorChar) + 1);
}
int count = 1;
@@ -95,8 +315,8 @@ public class Jalview2XML
{
if (shortName.endsWith("_" + (count - 1)))
{
- shortName = shortName.substring(0,
- shortName.lastIndexOf("_"));
+ shortName = shortName
+ .substring(0, shortName.lastIndexOf("_"));
}
shortName = shortName.concat("_" + count);
@@ -113,75 +333,94 @@ public class Jalview2XML
int ap, apSize = af.alignPanels.size();
for (ap = 0; ap < apSize; ap++)
{
- AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
- elementAt(ap);
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
+ .elementAt(ap);
+ String fileName = apSize == 1 ? shortName : ap + shortName;
+ if (!fileName.endsWith(".xml"))
+ {
+ fileName = fileName + ".xml";
+ }
- SaveState(apanel,
- apSize == 1 ? shortName : ap + shortName,
- jout, out);
+ SaveState(apanel, fileName, jout);
}
}
}
-
- out.close();
+ try
+ {
+ jout.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
jout.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
+ // TODO: inform user of the problem - they need to know if their data was
+ // not saved !
+ if (errorMessage == null)
+ {
+ errorMessage = "Couldn't write Jalview Archive - see error output for details";
+ }
ex.printStackTrace();
}
}
// USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
public boolean SaveAlignment(AlignFrame af, String jarFile,
- String fileName)
+ String fileName)
{
try
{
int ap, apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
for (ap = 0; ap < apSize; ap++)
{
- AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap);
-
- SaveState(apanel,
- apSize == 1 ? fileName : fileName + ap,
- jout, out);
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
+ .elementAt(ap);
+ String jfileName = apSize == 1 ? fileName : fileName + ap;
+ if (!jfileName.endsWith(".xml"))
+ {
+ jfileName = jfileName + ".xml";
+ }
+ SaveState(apanel, jfileName, jout);
}
- out.close();
+ try
+ {
+ jout.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
jout.close();
return true;
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
+ errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
ex.printStackTrace();
return false;
}
}
/**
- * DOCUMENT ME!
- *
- * @param af DOCUMENT ME!
- * @param timeStamp DOCUMENT ME!
- * @param fileName DOCUMENT ME!
- * @param jout DOCUMENT ME!
- * @param out DOCUMENT ME!
+ * create a JalviewModel from an algnment view and marshall it to a
+ * JarOutputStream
+ *
+ * @param ap
+ * panel to create jalview model for
+ * @param fileName
+ * name of alignment panel written to output stream
+ * @param jout
+ * jar output stream
+ * @param out
+ * jar entry name
*/
- public JalviewModel SaveState(AlignmentPanel ap,
- String fileName,
- JarOutputStream jout,
- PrintWriter out)
+ public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+ JarOutputStream jout)
{
- if (seqRefIds == null)
- {
- seqRefIds = new Hashtable();
- }
-
+ initSeqRefs();
+ Vector jmolViewIds = new Vector(); //
Vector userColours = new Vector();
AlignViewport av = ap.av;
@@ -192,9 +431,9 @@ public class Jalview2XML
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
- jalview.datamodel.AlignmentI jal = av.alignment;
+ jalview.datamodel.AlignmentI jal = av.getAlignment();
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
jal = jal.getHiddenSequences().getFullAlignment();
}
@@ -205,46 +444,56 @@ public class Jalview2XML
vamsasSet.setGapChar(jal.getGapCharacter() + "");
+ if (jal.getDataset() != null)
+ {
+ // dataset id is the dataset's hashcode
+ vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
+ }
+ if (jal.getProperties() != null)
+ {
+ Enumeration en = jal.getProperties().keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ SequenceSetProperties ssp = new SequenceSetProperties();
+ ssp.setKey(key);
+ ssp.setValue(jal.getProperties().get(key).toString());
+ vamsasSet.addSequenceSetProperties(ssp);
+ }
+ }
+
JSeq jseq;
- Vector pdbfiles = null;
+ Set calcIdSet = new HashSet();
- //SAVE SEQUENCES
- int id = 0;
+ // SAVE SEQUENCES
+ String id = "";
jalview.datamodel.SequenceI jds;
for (int i = 0; i < jal.getHeight(); i++)
{
jds = jal.getSequenceAt(i);
- id = jds.hashCode();
+ id = seqHash(jds);
- if (seqRefIds.get(id + "") != null)
+ if (seqRefIds.get(id) != null)
{
-
+ // This happens for two reasons: 1. multiple views are being serialised.
+ // 2. the hashCode has collided with another sequence's code. This DOES
+ // HAPPEN! (PF00072.15.stk does this)
+ // JBPNote: Uncomment to debug writing out of files that do not read
+ // back in due to ArrayOutOfBoundExceptions.
+ // System.err.println("vamsasSeq backref: "+id+"");
+ // System.err.println(jds.getName()+"
+ // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(jds));
+ // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+ // System.err.println(rsq.getName()+"
+ // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(rsq));
}
else
{
- vamsasSeq = new Sequence();
- vamsasSeq.setId(id + "");
- vamsasSeq.setName(jds.getName());
- vamsasSeq.setSequence(jds.getSequenceAsString());
- vamsasSeq.setDescription(jds.getDescription());
-
- if (jds.getDatasetSequence().getDBRef() != null)
- {
- jalview.datamodel.DBRefEntry[] dbrefs =
- jds.getDatasetSequence().getDBRef();
-
- for (int d = 0; d < dbrefs.length; d++)
- {
- DBRef dbref = new DBRef();
- dbref.setSource(dbrefs[d].getSource());
- dbref.setVersion(dbrefs[d].getVersion());
- dbref.setAccessionId(dbrefs[d].getAccessionId());
- vamsasSeq.addDBRef(dbref);
- }
- }
-
+ vamsasSeq = createVamsasSequence(id, jds);
vamsasSet.addSequence(vamsasSeq);
- seqRefIds.put(id + "", jal.getSequenceAt(i));
+ seqRefIds.put(id, jds);
}
jseq = new JSeq();
@@ -252,27 +501,22 @@ public class Jalview2XML
jseq.setEnd(jds.getEnd());
jseq.setColour(av.getSequenceColour(jds).getRGB());
- jseq.setId(id);
+ jseq.setId(id); // jseq id should be a string not a number
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
+ jseq.setHidden(av.getAlignment().getHiddenSequences().isHidden(jds));
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
+ if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
{
- jalview.datamodel.SequenceI[] reps =
- ( (jalview.datamodel.SequenceGroup)
- av.hiddenRepSequences.get(
- jal.getSequenceAt(i))).getSequencesInOrder(jal);
+ jalview.datamodel.SequenceI[] reps = av.getRepresentedSequences(
+ jal.getSequenceAt(i)).getSequencesInOrder(jal);
for (int h = 0; h < reps.length; h++)
{
if (reps[h] != jal.getSequenceAt(i))
{
- jseq.addHiddenSequences(
- jal.findIndex(reps[h])
- );
+ jseq.addHiddenSequences(jal.findIndex(reps[h]));
}
}
}
@@ -280,8 +524,8 @@ public class Jalview2XML
if (jds.getDatasetSequence().getSequenceFeatures() != null)
{
- jalview.datamodel.SequenceFeature[] sf
- = jds.getDatasetSequence().getSequenceFeatures();
+ jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
+ .getSequenceFeatures();
int index = 0;
while (index < sf.length)
{
@@ -312,8 +556,7 @@ public class Jalview2XML
key = keys.nextElement().toString();
OtherData keyValue = new OtherData();
keyValue.setKey(key);
- keyValue.setValue(
- sf[index].otherDetails.get(key).toString());
+ keyValue.setValue(sf[index].otherDetails.get(key).toString());
features.addOtherData(keyValue);
}
}
@@ -329,46 +572,91 @@ public class Jalview2XML
while (en.hasMoreElements())
{
Pdbids pdb = new Pdbids();
- jalview.datamodel.PDBEntry entry
- = (jalview.datamodel.PDBEntry) en.nextElement();
+ jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
+ .nextElement();
pdb.setId(entry.getId());
pdb.setType(entry.getType());
- AppJMol jmol;
- //This must have been loaded, is it still visible?
+ AppJmol jmol;
+ // 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 AppJmol)
{
- jmol = (AppJMol) frames[f];
- if (!jmol.pdbentry.getId().equals(entry.getId()))
- continue;
-
- StructureState state = new StructureState();
- state.setVisible(true);
- state.setXpos(jmol.getX());
- state.setYpos(jmol.getY());
- state.setWidth(jmol.getWidth());
- state.setHeight(jmol.getHeight());
-
- state.setContent(jmol.viewer.getStateInfo().replaceAll("\n", ""));
-
- for (int s = 0; s < jmol.sequence.length; s++)
+ jmol = (AppJmol) frames[f];
+ for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++)
{
- if (jal.findIndex(jmol.sequence[s]) > -1)
+ 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()))
{
- pdb.addStructureState(state);
+ 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);
+ }
}
}
}
}
-
- if (entry.getFile() != null)
+ if (matchedFile != null || entry.getFile() != null)
{
- pdb.setFile(entry.getFile());
+ if (entry.getFile() != null)
+ {
+ // use entry's file
+ matchedFile = entry.getFile();
+ }
+ pdb.setFile(matchedFile); // entry.getFile());
if (pdbfiles == null)
{
pdbfiles = new Vector();
@@ -379,23 +667,23 @@ public class Jalview2XML
pdbfiles.addElement(entry.getId());
try
{
- File file = new File(entry.getFile());
+ File file = new File(matchedFile);
if (file.exists() && jout != null)
{
- byte[] data = new byte[ (int) file.length()];
+ byte[] data = new byte[(int) file.length()];
jout.putNextEntry(new JarEntry(entry.getId()));
- DataInputStream dis = new DataInputStream(new
- FileInputStream(file));
+ 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)
+ } catch (Exception ex)
{
- ex.printStackTrace();
+ ex.printStackTrace();
}
}
@@ -424,13 +712,50 @@ public class Jalview2XML
jms.addJSeq(jseq);
}
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- jal = av.alignment;
+ jal = av.getAlignment();
+ }
+ // SAVE MAPPINGS
+ if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
+ {
+ jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
+ for (int i = 0; i < jac.length; i++)
+ {
+ AlcodonFrame alc = new AlcodonFrame();
+ vamsasSet.addAlcodonFrame(alc);
+ for (int p = 0; p < jac[i].aaWidth; p++)
+ {
+ 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();
+ 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
- ///////////////////////////////////
+ // SAVE TREES
+ // /////////////////////////////////
if (av.currentTree != null)
{
// FIND ANY ASSOCIATED TREES
@@ -445,11 +770,11 @@ public class Jalview2XML
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.treeCanvas.av.alignment == jal)
+ if (tp.treeCanvas.av.getAlignment() == jal)
{
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
- tree.setCurrentTree( (av.currentTree == tp.getTree()));
+ tree.setCurrentTree((av.currentTree == tp.getTree()));
tree.setNewick(tp.getTree().toString());
tree.setThreshold(tp.treeCanvas.threshold);
@@ -466,18 +791,22 @@ public class Jalview2XML
tree.setWidth(tp.getWidth());
tree.setXpos(tp.getX());
tree.setYpos(tp.getY());
-
+ tree.setId(makeHashCode(tp, null));
jms.addTree(tree);
}
}
}
}
}
-
- //SAVE ANNOTATIONS
+ // SAVE ANNOTATIONS
+ /**
+ * store forward refs from an annotationRow to any groups
+ */
+ IdentityHashMap groupRefs = new IdentityHashMap();
if (jal.getAlignmentAnnotation() != null)
{
- jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
+ jalview.datamodel.AlignmentAnnotation[] aa = jal
+ .getAlignmentAnnotation();
for (int i = 0; i < aa.length; i++)
{
@@ -490,22 +819,35 @@ public class Jalview2XML
an.setId(aa[i].annotationId);
- if (aa[i] == av.quality ||
- aa[i] == av.conservation ||
- aa[i] == av.consensus)
- {
- an.setLabel(aa[i].label);
- an.setGraph(true);
- vamsasSet.addAnnotation(an);
- continue;
- }
+ 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)
{
@@ -528,50 +870,91 @@ public class Jalview2XML
an.setLabel(aa[i].label);
- AnnotationElement ae;
+ 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());
+ }
- for (int a = 0; a < aa[i].annotations.length; a++)
+ if (aa[i].getCalcId() != null)
{
- if ( (aa[i] == null) || (aa[i].annotations[a] == 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++)
{
- continue;
- }
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))
+ {
+ continue;
+ }
- ae = new AnnotationElement();
- ae.setDescription(aa[i].annotations[a].description);
- ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
- ae.setValue(aa[i].annotations[a].value);
- ae.setPosition(a);
- ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
- "");
+ 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 (aa[i].annotations[a].colour != java.awt.Color.black)
- {
- ae.setColour(aa[i].annotations[a].colour.getRGB());
- }
+ if (!Float.isNaN(aa[i].annotations[a].value))
+ ae.setValue(aa[i].annotations[a].value);
- an.addAnnotationElement(ae);
- }
+ ae.setPosition(a);
+ if (aa[i].annotations[a].secondaryStructure != ' '
+ && aa[i].annotations[a].secondaryStructure != '\0')
+ ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ + "");
+
+ if (aa[i].annotations[a].colour != null
+ && aa[i].annotations[a].colour != java.awt.Color.black)
+ {
+ ae.setColour(aa[i].annotations[a].colour.getRGB());
+ }
+ an.addAnnotationElement(ae);
+ if (aa[i].autoCalculated)
+ {
+ // only write one non-null entry into the annotation row -
+ // sufficient to get the visualization attributes necessary to
+ // display data
+ continue;
+ }
+ }
+ }
+ else
+ {
+ an.setScoreOnly(true);
+ }
vamsasSet.addAnnotation(an);
}
}
-
- //SAVE GROUPS
+ // SAVE GROUPS
if (jal.getGroups() != null)
{
JGroup[] groups = new JGroup[jal.getGroups().size()];
-
- for (int i = 0; i < groups.length; i++)
+ int i = -1;
+ for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
{
- groups[i] = new JGroup();
+ groups[++i] = new JGroup();
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
- jal.getGroups()
- .elementAt(i);
groups[i].setStart(sg.getStartRes());
groups[i].setEnd(sg.getEndRes());
groups[i].setName(sg.getName());
+ if (groupRefs.containsKey(sg))
+ {
+ // group has references so set it's ID field
+ groups[i].setId(groupRefs.get(sg).toString());
+ }
if (sg.cs != null)
{
if (sg.cs.conservationApplied())
@@ -580,32 +963,30 @@ public class Jalview2XML
if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
- groups[i].setColour(SetUserColourScheme(sg.cs,
- userColours,
- jms));
+ groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+ jms));
}
else
{
- groups[i].setColour(ColourSchemeProperty.getColourName(sg.
- cs));
+ groups[i]
+ .setColour(ColourSchemeProperty.getColourName(sg.cs));
}
}
else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
{
- groups[i].setColour(
- ColourSchemeProperty.getColourName(
- ( (jalview.schemes.AnnotationColourGradient) sg.cs).
- getBaseColour()));
+ groups[i]
+ .setColour(ColourSchemeProperty
+ .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
+ .getBaseColour()));
}
else if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
- groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
- jms));
+ groups[i]
+ .setColour(SetUserColourScheme(sg.cs, userColours, jms));
}
else
{
- groups[i].setColour(ColourSchemeProperty.getColourName(
- sg.cs));
+ groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
}
groups[i].setPidThreshold(sg.cs.getThreshold());
@@ -618,27 +999,31 @@ public class Jalview2XML
groups[i].setTextCol1(sg.textColour.getRGB());
groups[i].setTextCol2(sg.textColour2.getRGB());
groups[i].setTextColThreshold(sg.thresholdTextColour);
-
+ groups[i].setShowUnconserved(sg.getShowNonconserved());
+ groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+ groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
+ groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
+ groups[i].setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
for (int s = 0; s < sg.getSize(); s++)
{
- jalview.datamodel.Sequence seq =
- (jalview.datamodel.Sequence) sg.getSequenceAt(s);
- groups[i].addSeq(seq.hashCode());
+ jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
+ .getSequenceAt(s);
+ groups[i].addSeq(seqHash(seq));
}
}
jms.setJGroup(groups);
}
- ///////////SAVE VIEWPORT
+ // /////////SAVE VIEWPORT
Viewport view = new Viewport();
view.setTitle(ap.alignFrame.getTitle());
- view.setSequenceSetId(av.getSequenceSetId());
+ 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);
@@ -660,13 +1045,12 @@ public class Jalview2XML
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
- userColours, jms));
+ userColours, jms));
}
- else if (av.getGlobalColourScheme() instanceof jalview.schemes.
- AnnotationColourGradient)
+ else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
{
- jalview.schemes.AnnotationColourGradient acg
- = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme();
+ jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
+ .getGlobalColourScheme();
AnnotationColours ac = new AnnotationColours();
ac.setAboveThreshold(acg.getAboveThreshold());
@@ -675,11 +1059,12 @@ public class Jalview2XML
if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
{
ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
- userColours, jms));
+ userColours, jms));
}
else
{
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
+ ac.setColourScheme(ColourSchemeProperty.getColourName(acg
+ .getBaseColour()));
}
ac.setMaxColour(acg.getMaxColour().getRGB());
@@ -689,8 +1074,8 @@ public class Jalview2XML
}
else
{
- view.setBgColour(ColourSchemeProperty.getColourName(
- av.getGlobalColourScheme()));
+ view.setBgColour(ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
}
ColourSchemeI cs = av.getGlobalColourScheme();
@@ -725,46 +1110,75 @@ public class Jalview2XML
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();
+ jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- String[] renderOrder =
- ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+ String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
Vector settingsAdded = new Vector();
- for (int ro = 0; ro < renderOrder.length; ro++)
+ Object gstyle = null;
+ GraduatedColor gcol = null;
+ if (renderOrder != null)
{
- Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
- setting.setColour(
- ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).
- getRGB()
- );
+ for (int ro = 0; ro < renderOrder.length; ro++)
+ {
+ gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getFeatureStyle(renderOrder[ro]);
+ Setting setting = new Setting();
+ setting.setType(renderOrder[ro]);
+ if (gstyle instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) gstyle;
+ setting.setColour(gcol.getMaxColor().getRGB());
+ setting.setMincolour(gcol.getMinColor().getRGB());
+ setting.setMin(gcol.getMin());
+ setting.setMax(gcol.getMax());
+ setting.setColourByLabel(gcol.isColourByLabel());
+ setting.setAutoScale(gcol.isAutoScale());
+ setting.setThreshold(gcol.getThresh());
+ setting.setThreshstate(gcol.getThreshType());
+ }
+ else
+ {
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(renderOrder[ro]).getRGB());
+ }
- setting.setDisplay(
- av.featuresDisplayed.containsKey(renderOrder[ro])
- );
- float rorder=ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(renderOrder[ro]);
- if (rorder>-1) {
- setting.setOrder(rorder);
+ setting.setDisplay(av.featuresDisplayed
+ .containsKey(renderOrder[ro]));
+ float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getOrder(renderOrder[ro]);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(renderOrder[ro]);
}
- fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
}
-
- //Make sure we save none displayed feature settings
- Enumeration en =
- ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
- while (en.hasMoreElements())
+
+ // Make sure we save none displayed feature settings
+ Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+ .keySet().iterator();
+ while (en.hasNext())
{
- String key = en.nextElement().toString();
+ String key = en.next().toString();
if (settingsAdded.contains(key))
{
continue;
@@ -772,31 +1186,33 @@ public class Jalview2XML
Setting setting = new Setting();
setting.setType(key);
- setting.setColour(
- ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
- );
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(key).getRGB());
setting.setDisplay(false);
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(key);
- if (rorder>-1)
+ 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.keys();
- Vector groupsAdded=new Vector();
- while (en.hasMoreElements())
+ en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+ .keySet().iterator();
+ Vector groupsAdded = new Vector();
+ while (en.hasNext())
{
- String grp = en.nextElement().toString();
- if (groupsAdded.contains(grp))
+ String grp = en.next().toString();
+ if (groupsAdded.contains(grp))
{
continue;
}
Group g = new Group();
g.setName(grp);
- g.setDisplay(((Boolean)ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.get(grp)).booleanValue());
+ g.setDisplay(((Boolean) ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+ .get(grp)).booleanValue());
fs.addGroup(g);
groupsAdded.addElement(grp);
}
@@ -804,16 +1220,40 @@ public class Jalview2XML
}
- if (av.hasHiddenColumns)
+ 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++)
+ {
+ int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+ .elementAt(c);
+ HiddenColumns hc = new HiddenColumns();
+ hc.setStart(region[0]);
+ hc.setEnd(region[1]);
+ view.addHiddenColumns(hc);
+ }
+ }
+ }
+ if (calcIdSet.size() > 0)
{
- for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
+ for (String calcId : calcIdSet)
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
- elementAt(c);
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- view.addHiddenColumns(hc);
+ if (calcId.trim().length() > 0)
+ {
+ CalcIdParam cidp = createCalcIdParam(calcId, av);
+ // Some calcIds have no parameters.
+ if (cidp != null)
+ {
+ view.addCalcIdParam(cidp);
+ }
+ }
}
}
@@ -822,52 +1262,324 @@ public class Jalview2XML
object.setJalviewModelSequence(jms);
object.getVamsasModel().addSequenceSet(vamsasSet);
- if (out != null)
+ if (jout != null && fileName != null)
{
- //We may not want to right the object to disk,
- //eg we can copy the alignViewport to a new view object
- //using save and then load
+ // We may not want to write the object to disk,
+ // eg we can copy the alignViewport to a new view object
+ // using save and then load
try
{
- if (!fileName.endsWith(".xml"))
- {
- fileName = fileName + ".xml";
- }
-
JarEntry entry = new JarEntry(fileName);
jout.putNextEntry(entry);
-
- object.marshal(out);
- }
- catch (Exception ex)
+ PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
+ "UTF-8"));
+ org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
+ pout);
+ marshaller.marshal(object);
+ pout.flush();
+ jout.closeEntry();
+ } catch (Exception ex)
{
+ // TODO: raise error in GUI if marshalling failed.
ex.printStackTrace();
}
}
return object;
}
+ private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
+ {
+ AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
+ if (settings != null)
+ {
+ CalcIdParam vCalcIdParam = new CalcIdParam();
+ vCalcIdParam.setCalcId(calcId);
+ vCalcIdParam.addServiceURL(settings.getServiceURI());
+ // generic URI allowing a third party to resolve another instance of the
+ // service used for this calculation
+ for (String urls : settings.getServiceURLs())
+ {
+ vCalcIdParam.addServiceURL(urls);
+ }
+ vCalcIdParam.setVersion("1.0");
+ if (settings.getPreset() != null)
+ {
+ WsParamSetI setting = settings.getPreset();
+ vCalcIdParam.setName(setting.getName());
+ vCalcIdParam.setDescription(setting.getDescription());
+ }
+ else
+ {
+ vCalcIdParam.setName("");
+ vCalcIdParam.setDescription("Last used parameters");
+ }
+ // need to be able to recover 1) settings 2) user-defined presets or
+ // recreate settings from preset 3) predefined settings provided by
+ // service - or settings that can be transferred (or discarded)
+ vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n",
+ "|\\n|"));
+ vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
+ // todo - decide if updateImmediately is needed for any projects.
+
+ return vCalcIdParam;
+ }
+ return null;
+ }
+
+ private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
+ AlignViewport av)
+ {
+ if (calcIdParam.getVersion().equals("1.0"))
+ {
+ Jws2Instance service = Jws2Discoverer.getDiscoverer()
+ .getPreferredServiceFor(calcIdParam.getServiceURL());
+ if (service != null)
+ {
+ WsParamSetI parmSet = null;
+ try
+ {
+ parmSet = service.getParamStore().parseServiceParameterFile(
+ calcIdParam.getName(), calcIdParam.getDescription(),
+ calcIdParam.getServiceURL(),
+ calcIdParam.getParameters().replace("|\\n|", "\n"));
+ } catch (IOException x)
+ {
+ warn("Couldn't parse parameter data for "
+ + calcIdParam.getCalcId(), x);
+ return false;
+ }
+ List argList = null;
+ if (calcIdParam.getName().length() > 0)
+ {
+ parmSet = service.getParamStore()
+ .getPreset(calcIdParam.getName());
+ if (parmSet != null)
+ {
+ // TODO : check we have a good match with settings in AACon -
+ // otherwise we'll need to create a new preset
+ }
+ }
+ else
+ {
+ argList = parmSet.getArguments();
+ parmSet = null;
+ }
+ AAConSettings settings = new AAConSettings(
+ calcIdParam.isAutoUpdate(), service, parmSet, argList);
+ av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
+ calcIdParam.isNeedsUpdate());
+ return true;
+ }
+ else
+ {
+ warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ return false;
+ }
+ }
+ throw new Error("Unsupported Version for calcIdparam "
+ + calcIdParam.toString());
+ }
+
+ /**
+ * External mapping between jalview objects and objects yielding a valid and
+ * unique object ID string. This is null for normal Jalview project IO, but
+ * non-null when a jalview project is being read or written as part of a
+ * vamsas session.
+ */
+ IdentityHashMap jv2vobj = null;
+
+ /**
+ * Construct a unique ID for jvobj using either existing bindings or if none
+ * exist, the result of the hashcode call for the object.
+ *
+ * @param jvobj
+ * jalview data object
+ * @return unique ID for referring to jvobj
+ */
+ private String makeHashCode(Object jvobj, String altCode)
+ {
+ if (jv2vobj != null)
+ {
+ Object id = jv2vobj.get(jvobj);
+ if (id != null)
+ {
+ return id.toString();
+ }
+ // check string ID mappings
+ if (jvids2vobj != null && jvobj instanceof String)
+ {
+ id = jvids2vobj.get(jvobj);
+ }
+ if (id != null)
+ {
+ return id.toString();
+ }
+ // give up and warn that something has gone wrong
+ warn("Cannot find ID for object in external mapping : " + jvobj);
+ }
+ return altCode;
+ }
+
+ /**
+ * return local jalview object mapped to ID, if it exists
+ *
+ * @param idcode
+ * (may be null)
+ * @return null or object bound to idcode
+ */
+ private Object retrieveExistingObj(String idcode)
+ {
+ if (idcode != null && vobj2jv != null)
+ {
+ return vobj2jv.get(idcode);
+ }
+ return null;
+ }
+
+ /**
+ * binding from ID strings from external mapping table to jalview data model
+ * objects.
+ */
+ private Hashtable vobj2jv;
+
+ private Sequence createVamsasSequence(String id, SequenceI jds)
+ {
+ return createVamsasSequence(true, id, jds, null);
+ }
+
+ private Sequence createVamsasSequence(boolean recurse, String id,
+ SequenceI jds, SequenceI parentseq)
+ {
+ Sequence vamsasSeq = new Sequence();
+ vamsasSeq.setId(id);
+ vamsasSeq.setName(jds.getName());
+ vamsasSeq.setSequence(jds.getSequenceAsString());
+ vamsasSeq.setDescription(jds.getDescription());
+ jalview.datamodel.DBRefEntry[] dbrefs = null;
+ if (jds.getDatasetSequence() != null)
+ {
+ vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
+ if (jds.getDatasetSequence().getDBRef() != null)
+ {
+ dbrefs = jds.getDatasetSequence().getDBRef();
+ }
+ }
+ else
+ {
+ vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
+ // dataset sequences only
+ dbrefs = jds.getDBRef();
+ }
+ if (dbrefs != null)
+ {
+ for (int d = 0; d < dbrefs.length; d++)
+ {
+ DBRef dbref = new DBRef();
+ dbref.setSource(dbrefs[d].getSource());
+ dbref.setVersion(dbrefs[d].getVersion());
+ dbref.setAccessionId(dbrefs[d].getAccessionId());
+ if (dbrefs[d].hasMap())
+ {
+ Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+ jds, recurse);
+ dbref.setMapping(mp);
+ }
+ vamsasSeq.addDBRef(dbref);
+ }
+ }
+ return vamsasSeq;
+ }
+
+ private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
+ SequenceI parentseq, SequenceI jds, boolean recurse)
+ {
+ Mapping mp = null;
+ if (jmp.getMap() != null)
+ {
+ mp = new Mapping();
+
+ jalview.util.MapList mlst = jmp.getMap();
+ int r[] = mlst.getFromRanges();
+ for (int s = 0; s < r.length; s += 2)
+ {
+ MapListFrom mfrom = new MapListFrom();
+ mfrom.setStart(r[s]);
+ mfrom.setEnd(r[s + 1]);
+ mp.addMapListFrom(mfrom);
+ }
+ r = mlst.getToRanges();
+ for (int s = 0; s < r.length; s += 2)
+ {
+ MapListTo mto = new MapListTo();
+ mto.setStart(r[s]);
+ mto.setEnd(r[s + 1]);
+ mp.addMapListTo(mto);
+ }
+ mp.setMapFromUnit(mlst.getFromRatio());
+ mp.setMapToUnit(mlst.getToRatio());
+ if (jmp.getTo() != null)
+ {
+ MappingChoice mpc = new MappingChoice();
+ if (recurse
+ && (parentseq != jmp.getTo() || parentseq
+ .getDatasetSequence() != jmp.getTo()))
+ {
+ mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
+ jmp.getTo(), jds));
+ }
+ else
+ {
+ String jmpid = "";
+ SequenceI ps = null;
+ if (parentseq != jmp.getTo()
+ && parentseq.getDatasetSequence() != jmp.getTo())
+ {
+ // chaining dbref rather than a handshaking one
+ jmpid = seqHash(ps = jmp.getTo());
+ }
+ else
+ {
+ jmpid = seqHash(ps = parentseq);
+ }
+ mpc.setDseqFor(jmpid);
+ if (!seqRefIds.containsKey(mpc.getDseqFor()))
+ {
+ jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+ seqRefIds.put(mpc.getDseqFor(), ps);
+ }
+ else
+ {
+ jalview.bin.Cache.log.debug("reusing DseqFor ID");
+ }
+ }
+ mp.setMappingChoice(mpc);
+ }
+ }
+ return mp;
+ }
+
String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
- Vector userColours, JalviewModelSequence jms)
+ Vector userColours, JalviewModelSequence jms)
{
String id = null;
- jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
- cs;
-
+ jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
+ boolean newucs = false;
if (!userColours.contains(ucs))
{
userColours.add(ucs);
-
+ newucs = true;
+ }
+ id = "ucs" + userColours.indexOf(ucs);
+ if (newucs)
+ {
+ // actually create the scheme's entry in the XML model
java.awt.Color[] colours = ucs.getColours();
- jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.
- version2.UserColours();
- jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.
- schemabinding.version2.UserColourScheme();
+ jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
+ jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
for (int i = 0; i < colours.length; i++)
{
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
- version2.Colour();
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
col.setName(ResidueProperties.aa[i]);
col.setRGB(jalview.util.Format.getHexString(colours[i]));
jbucs.addColour(col);
@@ -877,15 +1589,13 @@ public class Jalview2XML
colours = ucs.getLowerCaseColours();
for (int i = 0; i < colours.length; i++)
{
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
- version2.Colour();
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
col.setName(ResidueProperties.aa[i].toLowerCase());
col.setRGB(jalview.util.Format.getHexString(colours[i]));
jbucs.addColour(col);
}
}
- id = "ucs" + userColours.indexOf(ucs);
uc.setId(id);
uc.setUserColourScheme(jbucs);
jms.addUserColours(uc);
@@ -895,7 +1605,7 @@ public class Jalview2XML
}
jalview.schemes.UserColourScheme GetUserColourScheme(
- JalviewModelSequence jms, String id)
+ JalviewModelSequence jms, String id)
{
UserColours[] uc = jms.getUserColours();
UserColours colours = null;
@@ -914,20 +1624,20 @@ public class Jalview2XML
for (int i = 0; i < 24; i++)
{
- newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour(i).getRGB(), 16));
+ newColours[i] = new java.awt.Color(Integer.parseInt(colours
+ .getUserColourScheme().getColour(i).getRGB(), 16));
}
- jalview.schemes.UserColourScheme ucs =
- new jalview.schemes.UserColourScheme(newColours);
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ newColours);
if (colours.getUserColourScheme().getColourCount() > 24)
{
newColours = new java.awt.Color[23];
for (int i = 0; i < 23; i++)
{
- newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
+ newColours[i] = new java.awt.Color(Integer.parseInt(colours
+ .getUserColourScheme().getColour(i + 24).getRGB(), 16));
}
ucs.setLowerCaseColours(newColours);
}
@@ -936,46 +1646,142 @@ public class Jalview2XML
}
/**
- * DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
+ * contains last error message (if any) encountered by XML loader.
+ */
+ String errorMessage = null;
+
+ /**
+ * flag to control whether the Jalview2XML_V1 parser should be deferred to if
+ * exceptions are raised during project XML parsing
+ */
+ public boolean attemptversion1parse = true;
+
+ /**
+ * Load a jalview project archive from a jar file
+ *
+ * @param file
+ * - HTTP URL or filename
*/
public AlignFrame LoadJalviewAlign(final String file)
{
- uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
jalview.gui.AlignFrame af = null;
- seqRefIds = new Hashtable();
- viewportsAdded = new Hashtable();
-
- Hashtable gatherToThisFrame = new Hashtable();
-
try
{
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
- URL url = null;
-
- if (file.startsWith("http://"))
+ // create list to store references for any new Jmol viewers created
+ newStructureViewers=new Vector();
+ // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+ // Workaround is to make sure caller implements the JarInputStreamProvider
+ // interface
+ // so we can re-open the jar input stream for each entry.
+
+ jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
+ af = LoadJalviewAlign(jprovider);
+
+ } catch (MalformedURLException e)
+ {
+ errorMessage = "Invalid URL format for '" + file + "'";
+ reportErrors();
+ }
+ finally {
+ try
{
- url = new URL(file);
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+ public void run()
+ {
+ setLoadingFinishedForNewStructureViewers();
+ };
+ });
+ } catch (Exception x)
+ {
+
}
+ }
+ return af;
+ }
- JarInputStream jin = null;
- JarEntry jarentry = null;
- int entryCount = 1;
+ private jarInputStreamProvider createjarInputStreamProvider(
+ final String file) throws MalformedURLException
+ {
+ URL url = null;
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded = null;
+ frefedSequence = null;
+
+ if (file.startsWith("http://"))
+ {
+ url = new URL(file);
+ }
+ final URL _url = url;
+ return new jarInputStreamProvider()
+ {
- do
+ @Override
+ public JarInputStream getJarInputStream() throws IOException
{
- if (url != null)
+ if (_url != null)
{
- jin = new JarInputStream(url.openStream());
+ return new JarInputStream(_url.openStream());
}
else
{
- jin = new JarInputStream(new FileInputStream(file));
+ return new JarInputStream(new FileInputStream(file));
}
+ }
+
+ @Override
+ public String getFilename()
+ {
+ return file;
+ }
+ };
+ }
+
+ /**
+ * Recover jalview session from a jalview project archive. Caller may
+ * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
+ * themselves. Any null fields will be initialised with default values,
+ * non-null fields are left alone.
+ *
+ * @param jprovider
+ * @return
+ */
+ public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
+ {
+ errorMessage = null;
+ if (uniqueSetSuffix == null)
+ {
+ uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
+ }
+ if (seqRefIds == null)
+ {
+ seqRefIds = new Hashtable();
+ }
+ if (viewportsAdded == null)
+ {
+ viewportsAdded = new Hashtable();
+ }
+ if (frefedSequence == null)
+ {
+ frefedSequence = new Vector();
+ }
+
+ jalview.gui.AlignFrame af = null;
+ Hashtable gatherToThisFrame = new Hashtable();
+ final String file = jprovider.getFilename();
+ try
+ {
+ JarInputStream jin = null;
+ JarEntry jarentry = null;
+ int entryCount = 1;
+ do
+ {
+ jin = jprovider.getJarInputStream();
for (int i = 0; i < entryCount; i++)
{
jarentry = jin.getNextJarEntry();
@@ -989,44 +1795,56 @@ public class Jalview2XML
Unmarshaller unmar = new Unmarshaller(object);
unmar.setValidation(false);
object = (JalviewModel) unmar.unmarshal(in);
-
- af = LoadFromObject(object, file, true);
- if (af.viewport.gatherViewsHere)
+ if (true) // !skipViewport(object))
{
- gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ af = LoadFromObject(object, file, true, jprovider);
+ if (af.viewport.gatherViewsHere)
+ {
+ gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ }
}
entryCount++;
}
else if (jarentry != null)
{
- //Some other file here.
+ // Some other file here.
entryCount++;
}
- }
- while (jarentry != null);
- }
- catch (java.net.UnknownHostException ex)
+ } while (jarentry != null);
+ resolveFrefedSequences();
+ } catch (java.io.FileNotFoundException ex)
{
ex.printStackTrace();
- System.err.println("Couldn't locate Jalview XML file : " +
- ex + "\n");
-
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ errorMessage = "Couldn't locate Jalview XML file : " + file;
+ System.err.println("Exception whilst loading jalview XML file : "
+ + ex + "\n");
+ } catch (java.net.UnknownHostException ex)
+ {
+ ex.printStackTrace();
+ errorMessage = "Couldn't locate Jalview XML file : " + file;
+ System.err.println("Exception whilst loading jalview XML file : "
+ + ex + "\n");
+ } catch (Exception ex)
+ {
+ System.err.println("Parsing as Jalview Version 2 file failed.");
+ ex.printStackTrace(System.err);
+ if (attemptversion1parse)
{
- public void run()
+ // Is Version 1 Jar file?
+ try
+ {
+ af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
+ } catch (Exception ex2)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't locate " + file,
- "URL not found",
- JOptionPane.WARNING_MESSAGE);
+ System.err.println("Exception whilst loading as jalviewXMLV1:");
+ ex2.printStackTrace();
+ af = null;
}
- });
- }
- catch (Exception ex)
- {
- //Is Version 1 Jar file?
- af = new Jalview2XML_V1().LoadJalviewAlign(file);
-
+ }
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
if (af != null)
{
System.out.println("Successfully loaded archive file");
@@ -1034,19 +1852,14 @@ public class Jalview2XML
}
ex.printStackTrace();
- System.err.println("Exception whilst loading jalview XML file : " +
- ex + "\n");
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Error loading " + file,
- "Error loading Jalview file",
- JOptionPane.WARNING_MESSAGE);
- }
- });
+ System.err.println("Exception whilst loading jalview XML file : "
+ + ex + "\n");
+ } catch (OutOfMemoryError e)
+ {
+ // Don't use the OOM Window here
+ errorMessage = "Out of memory loading jalview XML file";
+ System.err.println("Out of memory whilst loading jalview XML file");
+ e.printStackTrace();
}
if (Desktop.instance != null)
@@ -1055,17 +1868,64 @@ public class Jalview2XML
}
Enumeration en = gatherToThisFrame.elements();
- while(en.hasMoreElements())
+ while (en.hasMoreElements())
{
- Desktop.instance.gatherViews(
- (AlignFrame) en.nextElement());
+ Desktop.instance.gatherViews((AlignFrame) en.nextElement());
+ }
+ if (errorMessage != null)
+ {
+ reportErrors();
}
-
return af;
}
+ /**
+ * 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.
+ */
+ protected void reportErrors()
+ {
+ reportErrors(false);
+ }
+
+ protected void reportErrors(final boolean saving)
+ {
+ if (errorMessage != null)
+ {
+ final String finalErrorMessage = errorMessage;
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ finalErrorMessage, "Error "
+ + (saving ? "saving" : "loading")
+ + " Jalview file", JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ else
+ {
+ System.err.println("Problem loading Jalview file: " + errorMessage);
+ }
+ }
+ errorMessage = null;
+ }
+
Hashtable alreadyLoadedPDB;
- String loadPDBFile(String file, String pdbId)
+
+ /**
+ * when set, local views will be updated from view stored in JalviewXML
+ * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
+ * sync if this is set to true.
+ */
+ private final boolean updateLocalViews = false;
+
+ String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
{
if (alreadyLoadedPDB == null)
alreadyLoadedPDB = new Hashtable();
@@ -1075,41 +1935,47 @@ public class Jalview2XML
try
{
- JarInputStream jin = null;
-
- if (file.startsWith("http://"))
- {
- jin = new JarInputStream(new URL(file).openStream());
- }
- else
- {
- jin = new JarInputStream(new FileInputStream(file));
- }
+ JarInputStream jin = jprovider.getJarInputStream();
+ /*
+ * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
+ * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
+ * FileInputStream(jprovider)); }
+ */
JarEntry entry = null;
do
{
entry = jin.getNextJarEntry();
- }
- while (!entry.getName().equals(pdbId));
-
- BufferedReader in = new BufferedReader(new InputStreamReader(jin));
- File outFile = File.createTempFile("jalview_pdb", ".txt");
- outFile.deleteOnExit();
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
+ } while (entry != null && !entry.getName().equals(pdbId));
+ if (entry != null)
+ {
+ BufferedReader in = new BufferedReader(new InputStreamReader(jin));
+ File outFile = File.createTempFile("jalview_pdb", ".txt");
+ outFile.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
- while ( (data = in.readLine()) != null)
+ while ((data = in.readLine()) != null)
+ {
+ out.println(data);
+ }
+ try
+ {
+ out.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
+ out.close();
+ String t = outFile.getAbsolutePath();
+ alreadyLoadedPDB.put(pdbId, t);
+ return t;
+ }
+ else
{
- out.println(data);
+ warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
}
- out.close();
-
- alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
- return outFile.getAbsolutePath();
-
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
@@ -1117,9 +1983,40 @@ public class Jalview2XML
return null;
}
- AlignFrame LoadFromObject(JalviewModel object,
- String file,
- boolean loadTreesAndStructures)
+ private class JvAnnotRow
+ {
+ public JvAnnotRow(int i, AlignmentAnnotation jaa)
+ {
+ order = i;
+ template = jaa;
+ }
+
+ /**
+ * persisted version of annotation row from which to take vis properties
+ */
+ public jalview.datamodel.AlignmentAnnotation template;
+
+ /**
+ * original position of the annotation row in the alignment
+ */
+ public int order;
+ }
+
+ /**
+ * Load alignment frame from jalview XML DOM object
+ *
+ * @param object
+ * DOM
+ * @param file
+ * filename source string
+ * @param loadTreesAndStructures
+ * when false only create Viewport
+ * @param jprovider
+ * data source provider
+ * @return alignment frame created from view stored in DOM
+ */
+ AlignFrame LoadFromObject(JalviewModel object, String file,
+ boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
Sequence[] vamsasSeq = vamsasSet.getSequence();
@@ -1127,9 +2024,8 @@ public class Jalview2XML
JalviewModelSequence jms = object.getJalviewModelSequence();
Viewport view = jms.getViewport(0);
-
- //////////////////////////////////
- //LOAD SEQUENCES
+ // ////////////////////////////////
+ // LOAD SEQUENCES
Vector hiddenSeqs = null;
jalview.datamodel.Sequence jseq;
@@ -1139,24 +2035,27 @@ public class Jalview2XML
boolean multipleView = false;
JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+ int vi = 0; // counter in vamsasSeq array
for (int i = 0; i < JSEQ.length; i++)
{
- String seqId = JSEQ[i].getId() + "";
+ String seqId = JSEQ[i].getId();
if (seqRefIds.get(seqId) != null)
{
- tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ tmpseqs.add(seqRefIds.get(seqId));
multipleView = true;
}
else
{
- jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
- vamsasSeq[i].getSequence());
- jseq.setDescription(vamsasSeq[i].getDescription());
+ 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());
- seqRefIds.put(vamsasSeq[i].getId(), jseq);
+ jseq.setVamsasId(uniqueSetSuffix + seqId);
+ seqRefIds.put(vamsasSeq[vi].getId(), jseq);
tmpseqs.add(jseq);
+ vi++;
}
if (JSEQ[i].getHidden())
@@ -1166,33 +2065,49 @@ public class Jalview2XML
hiddenSeqs = new Vector();
}
- hiddenSeqs.addElement(
- (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ hiddenSeqs.addElement(seqRefIds.get(seqId));
}
}
- ///SequenceFeatures are added to the DatasetSequence,
- // so we must create the dataset before loading features
- /////////////////////////////////
-
-
- jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
- tmpseqs.size()];
+ // /
+ // Create the alignment object from the sequence set
+ // ///////////////////////////////
+ jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
+ .size()];
tmpseqs.toArray(orderedSeqs);
- jalview.datamodel.Alignment al =
- new jalview.datamodel.Alignment(orderedSeqs);
-
- al.setDataset(null);
- /////////////////////////////////
-
+ jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
+ orderedSeqs);
- Hashtable pdbloaded = new Hashtable();
+ // / Add the alignment properties
+ for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
+ {
+ SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
+ al.setProperty(ssp.getKey(), ssp.getValue());
+ }
- if (!multipleView)
+ // /
+ // SequenceFeatures are added to the DatasetSequence,
+ // so we must create or recover the dataset before loading features
+ // ///////////////////////////////
+ if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
{
+ // older jalview projects do not have a dataset id.
+ al.setDataset(null);
+ }
+ else
+ {
+ recoverDatasetFor(vamsasSet, al);
+ }
+ // ///////////////////////////////
+
+ Hashtable pdbloaded = new Hashtable();
+ 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)
@@ -1200,11 +2115,10 @@ public class Jalview2XML
Features[] features = JSEQ[i].getFeatures();
for (int f = 0; f < features.length; f++)
{
- jalview.datamodel.SequenceFeature sf
- = new jalview.datamodel.SequenceFeature(features[f].getType(),
- features[f].getDescription(), features[f].getStatus(),
- features[f].getBegin(), features[f].getEnd(),
- features[f].getFeatureGroup());
+ jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
+ features[f].getType(), features[f].getDescription(),
+ features[f].getStatus(), features[f].getBegin(),
+ features[f].getEnd(), features[f].getFeatureGroup());
sf.setScore(features[f].getScore());
for (int od = 0; od < features[f].getOtherDataCount(); od++)
@@ -1224,21 +2138,23 @@ public class Jalview2XML
al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
}
}
-
+ if (vamsasSeq[i].getDBRefCount() > 0)
+ {
+ addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
+ }
if (JSEQ[i].getPdbidsCount() > 0)
{
Pdbids[] ids = JSEQ[i].getPdbids();
for (int p = 0; p < ids.length; p++)
{
- jalview.datamodel.PDBEntry entry = new jalview.datamodel.
- PDBEntry();
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
entry.setId(ids[p].getId());
entry.setType(ids[p].getType());
if (ids[p].getFile() != null)
{
if (!pdbloaded.containsKey(ids[p].getFile()))
{
- entry.setFile(loadPDBFile(file, ids[p].getId()));
+ entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
}
else
{
@@ -1249,29 +2165,79 @@ public class Jalview2XML
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
}
}
- if (vamsasSeq[i].getDBRefCount() > 0)
+ }
+ } // end !multipleview
+
+ // ///////////////////////////////
+ // LOAD SEQUENCE MAPPINGS
+
+ if (vamsasSet.getAlcodonFrameCount() > 0)
+ {
+ // TODO Potentially this should only be done once for all views of an
+ // alignment
+ 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)
{
- for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
+ Alcodon[] alcods = alc[i].getAlcodon();
+ for (int p = 0; p < cf.codons.length; p++)
{
- jalview.datamodel.DBRefEntry entry =
- new jalview.datamodel.DBRefEntry(
- vamsasSeq[i].getDBRef(d).getSource(),
- vamsasSeq[i].getDBRef(d).getVersion(),
- vamsasSeq[i].getDBRef(d).getAccessionId()
- );
- al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
+ 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;
+ }
+ }
+ }
+ 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());
+ // Load Mapping
+ jalview.datamodel.Mapping mapping = null;
+ // attach to dna sequence reference.
+ if (maps[m].getMapping() != null)
+ {
+ mapping = addMapping(maps[m].getMapping());
+ }
+ if (dnaseq != null)
+ {
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ else
+ {
+ // defer to later
+ frefedSequence.add(new Object[]
+ { maps[m].getDnasq(), cf, mapping });
+ }
}
-
}
+ al.addCodonFrame(cf);
}
+
}
- /////////////////////////////////
- //////////////////////////////////
- //LOAD ANNOTATIONS
- boolean hideQuality = true,
- hideConservation = true,
- hideConsensus = true;
+ // ////////////////////////////////
+ // LOAD ANNOTATIONS
+ ArrayList autoAlan = new ArrayList();
+ /**
+ * store any annotations which forward reference a group's ID
+ */
+ Hashtable> groupAnnotRefs = new Hashtable>();
if (vamsasSet.getAnnotationCount() > 0)
{
@@ -1279,96 +2245,194 @@ public class Jalview2XML
for (int i = 0; i < an.length; i++)
{
- if (an[i].getLabel().equals("Quality"))
- {
- hideQuality = false;
- continue;
- }
- else if (an[i].getLabel().equals("Conservation"))
+ /**
+ * test if annotation is automatically calculated for this view only
+ */
+ boolean autoForView = false;
+ if (an[i].getLabel().equals("Quality")
+ || an[i].getLabel().equals("Conservation")
+ || an[i].getLabel().equals("Consensus"))
{
- hideConservation = false;
- continue;
+ // Kludge for pre 2.5 projects which lacked the autocalculated flag
+ autoForView = true;
+ if (!an[i].hasAutoCalculated())
+ {
+ an[i].setAutoCalculated(true);
+ }
}
- else if (an[i].getLabel().equals("Consensus"))
+ if (autoForView
+ || (an[i].hasAutoCalculated() && an[i].isAutoCalculated()))
{
- hideConsensus = false;
- continue;
+ // remove ID - we don't recover annotation from other views for
+ // view-specific annotation
+ an[i].setId(null);
}
+ // set visiblity for other annotation in this view
if (an[i].getId() != null
- && annotationIds.containsKey(an[i].getId()))
+ && annotationIds.containsKey(an[i].getId()))
{
- al.addAnnotation(
- (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
- getId())
- );
+ jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) 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);
continue;
}
-
+ // Construct new annotation from model.
AnnotationElement[] ae = an[i].getAnnotationElement();
- jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
- al.getWidth()];
-
- for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
+ jalview.datamodel.Annotation[] anot = null;
+ java.awt.Color firstColour = null;
+ int anpos;
+ if (!an[i].getScoreOnly())
{
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
- getDisplayCharacter(),
- ae[aa].getDescription(),
- ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
- ae[aa].getSecondaryStructure().charAt(0),
- ae[aa].getValue());
- anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
- getColour());
- }
+ anot = new jalview.datamodel.Annotation[al.getWidth()];
+ for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
+ {
+ anpos = ae[aa].getPosition();
+
+ if (anpos >= anot.length)
+ continue;
+
+ anot[anpos] = new jalview.datamodel.Annotation(
+
+ ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
+ (ae[aa].getSecondaryStructure() == null || ae[aa]
+ .getSecondaryStructure().length() == 0) ? ' '
+ : ae[aa].getSecondaryStructure().charAt(0),
+ ae[aa].getValue()
+ );
+ // JBPNote: Consider verifying dataflow for IO of secondary
+ // structure annotation read from Stockholm files
+ // this was added to try to ensure that
+ // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
+ // {
+ // anot[ae[aa].getPosition()].displayCharacter = "";
+ // }
+ anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
+ if (firstColour == null)
+ {
+ firstColour = anot[anpos].colour;
+ }
+ }
+ }
jalview.datamodel.AlignmentAnnotation jaa = null;
if (an[i].getGraph())
{
+ float llim = 0, hlim = 0;
+ // if (autoForView || an[i].isAutoCalculated()) {
+ // hlim=11f;
+ // }
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot, 0, 0,
- an[i].getGraphType());
+ an[i].getDescription(), anot, llim, hlim,
+ an[i].getGraphType());
jaa.graphGroup = an[i].getGraphGroup();
-
+ jaa._linecolour = firstColour;
if (an[i].getThresholdLine() != null)
{
- jaa.setThreshold(new jalview.datamodel.GraphLine(
- an[i].getThresholdLine().getValue(),
- an[i].getThresholdLine().getLabel(),
- new java.awt.Color(an[i].getThresholdLine().getColour()))
- );
+ jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
+ .getThresholdLine().getValue(), an[i]
+ .getThresholdLine().getLabel(), new java.awt.Color(
+ an[i].getThresholdLine().getColour())));
}
-
+ if (autoForView || an[i].isAutoCalculated())
+ {
+ // Hardwire the symbol display line to ensure that labels for
+ // histograms are displayed
+ jaa.hasText = true;
+ }
}
else
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot);
+ an[i].getDescription(), anot);
+ jaa._linecolour = firstColour;
}
-
+ // register new annotation
if (an[i].getId() != null)
{
annotationIds.put(an[i].getId(), jaa);
jaa.annotationId = an[i].getId();
}
-
+ // recover sequence association
if (an[i].getSequenceRef() != null)
{
- jaa.createSequenceMapping(
- al.findName(an[i].getSequenceRef()), 1, true
- );
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ if (al.findName(an[i].getSequenceRef()) != null)
+ {
+ jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
+ 1, true);
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ }
+ }
+ // and make a note of any group association
+ if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
+ {
+ ArrayList aal = groupAnnotRefs
+ .get(an[i].getGroupRef());
+ if (aal == null)
+ {
+ aal = new ArrayList();
+ groupAnnotRefs.put(an[i].getGroupRef(), aal);
+ }
+ aal.add(jaa);
+ }
+
+ if (an[i].hasScore())
+ {
+ 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())
+ {
+ jaa.scaleColLabel = an[i].getScaleColLabels();
+ }
+ if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
+ {
+ // newer files have an 'autoCalculated' flag and store calculation
+ // state in viewport properties
+ jaa.autoCalculated = true; // means annotation will be marked for
+ // update at end of load.
+ }
+ if (an[i].hasGraphHeight())
+ {
+ jaa.graphHeight = an[i].getGraphHeight();
+ }
+ if (an[i].hasBelowAlignment())
+ {
+ jaa.belowAlignment = an[i].isBelowAlignment();
}
+ jaa.setCalcId(an[i].getCalcId());
- al.addAnnotation(jaa);
+ if (jaa.autoCalculated)
+ {
+ autoAlan.add(new JvAnnotRow(i, jaa));
+ }
+ else
+ // if (!autoForView)
+ {
+ // add autocalculated group annotation and any user created annotation
+ // for the view
+ al.addAnnotation(jaa);
+ }
}
}
- /////////////////////////
- //LOAD GROUPS
+ // ///////////////////////
+ // LOAD GROUPS
+ // Create alignment markup and styles for this view
if (jms.getJGroupCount() > 0)
{
JGroup[] groups = jms.getJGroup();
@@ -1385,8 +2449,7 @@ public class Jalview2XML
}
else
{
- cs = ColourSchemeProperty.getColour(al,
- groups[i].getColour());
+ cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
}
if (cs != null)
@@ -1400,8 +2463,8 @@ 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 = (jalview.datamodel.SequenceI) seqRefIds
+ .get(seqId);
if (ts != null)
{
@@ -1414,268 +2477,806 @@ public class Jalview2XML
continue;
}
- jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
- SequenceGroup(seqs,
- groups[i].getName(), cs, groups[i].getDisplayBoxes(),
- groups[i].getDisplayText(), groups[i].getColourText(),
- groups[i].getStart(), groups[i].getEnd());
+ jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
+ seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
+ groups[i].getDisplayText(), groups[i].getColourText(),
+ groups[i].getStart(), groups[i].getEnd());
- sg.setOutlineColour(new java.awt.Color(
- groups[i].getOutlineColour()));
+ sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
sg.textColour = new java.awt.Color(groups[i].getTextCol1());
sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
+ sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
+ .isShowUnconserved() : false);
sg.thresholdTextColour = groups[i].getTextColThreshold();
-
+ if (groups[i].hasShowConsensusHistogram())
+ {
+ sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
+ }
+ ;
+ if (groups[i].hasShowSequenceLogo())
+ {
+ sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
+ }
+ if (groups[i].hasNormaliseSequenceLogo())
+ {
+ sg.setNormaliseSequenceLogo(groups[i].isNormaliseSequenceLogo());
+ }
+ if (groups[i].hasIgnoreGapsinConsensus())
+ {
+ sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
+ }
if (groups[i].getConsThreshold() != 0)
{
jalview.analysis.Conservation c = new jalview.analysis.Conservation(
- "All",
- ResidueProperties.propHash, 3, sg.getSequences(null), 0,
- sg.getWidth() - 1);
+ "All", ResidueProperties.propHash, 3,
+ sg.getSequences(null), 0, sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
sg.cs.setConservation(c);
}
+ if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
+ {
+ // re-instate unique group/annotation row reference
+ ArrayList jaal = groupAnnotRefs
+ .get(groups[i].getId());
+ if (jaal != null)
+ {
+ for (jalview.datamodel.AlignmentAnnotation jaa : jaal)
+ {
+ jaa.groupRef = sg;
+ if (jaa.autoCalculated)
+ {
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Consensus for "))
+ {
+ sg.setConsensus(jaa);
+ }
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Conservation for "))
+ {
+ sg.setConservationRow(jaa);
+ }
+ }
+ }
+ }
+ }
al.addGroup(sg);
+
}
}
- /////////////////////////////////
+ // ///////////////////////////////
// LOAD VIEWPORT
- AlignFrame af = new AlignFrame(al,
- view.getWidth(),
- view.getHeight());
-
- af.setFileName(file, "Jalview");
-
- for (int i = 0; i < JSEQ.length; i++)
- {
- af.viewport.setSequenceColour(
- af.viewport.alignment.getSequenceAt(i),
- new java.awt.Color(
- JSEQ[i].getColour()));
- }
-
- //If we just load in the same jar file again, the sequenceSetId
- //will be the same, and we end up with multiple references
- //to the same sequenceSet. We must modify this id on load
- //so that each load of the file gives a unique id
+ // If we just load in the same jar file again, the sequenceSetId
+ // will be the same, and we end up with multiple references
+ // to the same sequenceSet. We must modify this id on load
+ // so that each load of the file gives a unique id
String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
-
- af.viewport.gatherViewsHere = view.getGatheredViews();
-
- if (view.getSequenceSetId() != null)
- {
- jalview.gui.AlignViewport av =
- (jalview.gui.AlignViewport)
- viewportsAdded.get(uniqueSeqSetId);
-
- af.viewport.sequenceSetID = uniqueSeqSetId;
- if (av != null)
- {
-
- af.viewport.historyList = av.historyList;
- af.viewport.redoList = av.redoList;
- }
- else
- {
- viewportsAdded.put(uniqueSeqSetId, af.viewport);
- }
-
- PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
- }
- if (hiddenSeqs != null)
+ String viewId = (view.getId() == null ? null : view.getId()
+ + uniqueSetSuffix);
+ AlignFrame af = null;
+ AlignViewport av = null;
+ // now check to see if we really need to create a new viewport.
+ if (multipleView && viewportsAdded.size() == 0)
{
- for (int s = 0; s < JSEQ.length; s++)
+ // We recovered an alignment for which a viewport already exists.
+ // TODO: fix up any settings necessary for overlaying stored state onto
+ // state recovered from another document. (may not be necessary).
+ // we may need a binding from a viewport in memory to one recovered from
+ // XML.
+ // and then recover its containing af to allow the settings to be applied.
+ // TODO: fix for vamsas demo
+ System.err
+ .println("About to recover a viewport for existing alignment: Sequence set ID is "
+ + uniqueSeqSetId);
+ Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
+ if (seqsetobj != null)
{
- jalview.datamodel.SequenceGroup hidden =
- new jalview.datamodel.SequenceGroup();
-
- for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
+ if (seqsetobj instanceof String)
{
- hidden.addSequence(
- al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
- , false
- );
+ uniqueSeqSetId = (String) seqsetobj;
+ System.err
+ .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
+ + uniqueSeqSetId);
+ }
+ else
+ {
+ System.err
+ .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
}
- 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);
}
-
- af.viewport.hideSequence(hseqs);
-
}
-
- if ( (hideConsensus || hideQuality || hideConservation)
- && al.getAlignmentAnnotation() != null)
+ AlignmentPanel ap = null;
+ boolean isnewview = true;
+ if (viewId != null)
{
- int hSize = al.getAlignmentAnnotation().length;
- for (int h = 0; h < hSize; h++)
+ // Check to see if this alignment already has a view id == viewId
+ jalview.gui.AlignmentPanel views[] = Desktop
+ .getAlignmentPanels(uniqueSeqSetId);
+ if (views != null && views.length > 0)
{
- if (
- (hideConsensus &&
- al.getAlignmentAnnotation()[h].label.equals("Consensus"))
- ||
- (hideQuality &&
- al.getAlignmentAnnotation()[h].label.equals("Quality"))
- ||
- (hideConservation &&
- al.getAlignmentAnnotation()[h].label.equals("Conservation")))
+ for (int v = 0; v < views.length; v++)
{
- al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
- hSize--;
- h--;
+ if (views[v].av.getViewId().equalsIgnoreCase(viewId))
+ {
+ // recover the existing alignpanel, alignframe, viewport
+ af = views[v].alignFrame;
+ av = views[v].av;
+ ap = views[v];
+ // TODO: could even skip resetting view settings if we don't want to
+ // change the local settings from other jalview processes
+ isnewview = false;
+ }
}
}
- af.alignPanel.adjustAnnotationHeight();
}
- if (view.getViewName() != null)
+ if (isnewview)
{
- af.viewport.viewName = view.getViewName();
- af.setInitialTabVisible();
+ af = loadViewport(file, JSEQ, hiddenSeqs, al, jms, view,
+ uniqueSeqSetId, viewId, autoAlan);
+ av = af.viewport;
+ ap = af.alignPanel;
}
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
- view.getHeight());
+ // LOAD TREES
+ // /////////////////////////////////////
+ if (loadTreesAndStructures && jms.getTreeCount() > 0)
+ {
+ try
+ {
+ for (int t = 0; t < jms.getTreeCount(); t++)
+ {
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.viewport.setAbovePIDThreshold(view.getPidSelected());
+ Tree tree = jms.getTree(t);
- af.viewport.setColourText(view.getShowColourText());
+ TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
+ if (tp == null)
+ {
+ tp = af.ShowNewickTree(
+ new jalview.io.NewickFile(tree.getNewick()),
+ tree.getTitle(), tree.getWidth(), tree.getHeight(),
+ tree.getXpos(), tree.getYpos());
+ if (tree.getId() != null)
+ {
+ // perhaps bind the tree id to something ?
+ }
+ }
+ else
+ {
+ // update local tree attributes ?
+ // TODO: should check if tp has been manipulated by user - if so its
+ // settings shouldn't be modified
+ tp.setTitle(tree.getTitle());
+ tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
+ .getWidth(), tree.getHeight()));
+ tp.av = av; // af.viewport; // TODO: verify 'associate with all
+ // views'
+ // works still
+ tp.treeCanvas.av = av; // af.viewport;
+ tp.treeCanvas.ap = ap; // af.alignPanel;
- 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.setRenderGaps(view.getRenderGaps());
- af.viewport.setWrapAlignment(view.getWrapAlignment());
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+ }
+ if (tp == null)
+ {
+ warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
+ continue;
+ }
- af.viewport.setShowBoxes(view.getShowBoxes());
+ tp.fitToWindow.setState(tree.getFitToWindow());
+ tp.fitToWindow_actionPerformed(null);
- af.viewport.setShowText(view.getShowText());
+ if (tree.getFontName() != null)
+ {
+ tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
+ .getFontStyle(), tree.getFontSize()));
+ }
+ else
+ {
+ tp.setTreeFont(new java.awt.Font(view.getFontName(), view
+ .getFontStyle(), tree.getFontSize()));
+ }
- af.viewport.textColour = new java.awt.Color(view.getTextCol1());
- af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
- af.viewport.thresholdTextColour = view.getTextColThreshold();
+ tp.showPlaceholders(tree.getMarkUnlinked());
+ tp.showBootstrap(tree.getShowBootstrap());
+ tp.showDistances(tree.getShowDistances());
- af.viewport.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
+ tp.treeCanvas.threshold = tree.getThreshold();
- ColourSchemeI cs = null;
+ if (tree.getCurrentTree())
+ {
+ af.viewport.setCurrentTree(tp.getTree());
+ }
+ }
- if (view.getBgColour() != null)
- {
- if (view.getBgColour().startsWith("ucs"))
+ } catch (Exception ex)
{
- cs = GetUserColourScheme(jms, view.getBgColour());
+ ex.printStackTrace();
}
- else if (view.getBgColour().startsWith("Annotation"))
+ }
+
+ // //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();
+
+ for (int i = 0; i < JSEQ.length; i++)
{
- //int find annotation
- for (int i = 0;
- i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+ if (JSEQ[i].getPdbidsCount() > 0)
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
- equals(view.getAnnotationColours().getAnnotation()))
+ Pdbids[] ids = JSEQ[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i].
- getThreshold() == null)
+ for (int s = 0; s < ids[p].getStructureStateCount(); s++)
{
- af.viewport.alignment.getAlignmentAnnotation()[i].
- setThreshold(
- new jalview.datamodel.GraphLine(
- view.getAnnotationColours().getThreshold(),
- "Threshold", java.awt.Color.black)
-
- );
- }
+ // 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());
- if (view.getAnnotationColours().getColourScheme().equals(
- "None"))
- {
- cs = new AnnotationColourGradient(
- af.viewport.alignment.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.alignment.getAlignmentAnnotation()[i],
- GetUserColourScheme(jms, view.getAnnotationColours().
- getColourScheme()),
- view.getAnnotationColours().getAboveThreshold()
- );
- }
- else
- {
- cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al,
- view.getAnnotationColours().
- getColourScheme()),
- view.getAnnotationColours().getAboveThreshold()
- );
- }
+ 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();
- // Also use these settings for all the groups
- if (al.getGroups() != null)
- {
- for (int g = 0; g < al.getGroups().size(); g++)
+ // 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)
{
- jalview.datamodel.SequenceGroup sg
- = (jalview.datamodel.SequenceGroup) al.getGroups().
- elementAt(g);
+ 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
+ }
- if (sg.cs == null)
+ // 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())
+ {
{
- continue;
+ jmoldat[1] = ids[p].getStructureState(s).getContent();
}
-
- /* if (view.getAnnotationColours().getColourScheme().equals("None"))
- {
- sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- new java.awt.Color(view.getAnnotationColours().
- getMinColour()),
- new java.awt.Color(view.getAnnotationColours().
- getMaxColour()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else*/
+ }
+ if (ids[p].getFile() != 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))
{
- sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- sg.cs,
- view.getAnnotationColours().getAboveThreshold()
- );
+ ((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
}
+ }
+ 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 Jmol views
+ for (Entry entry : jmolViewIds.entrySet())
+ {
+ 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();
+
+ // Search to see if we've already created this Jmol view
+ AppJmol comp = null;
+ JInternalFrame[] frames = null;
+ do
+ {
+ 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)
+ {
+ 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];
+ }
+ }
+ }
+ 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("\"");
+
+ }
+ newFileLoc.append(";");
+ }
+
+ 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);
+
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
}
}
- break;
}
+ else
+ // if (comp != null)
+ {
+ // 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) 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);
+ }
+ }
+ }
+ }
+ }
+ // and finally return.
+ return af;
+ }
+ Vector newStructureViewers=null;
+ protected void addNewStructureViewer(AppJmol sview)
+ {
+ if (newStructureViewers!=null)
+ {
+ sview.jmb.setFinishedLoadingFromArchive(false);
+ newStructureViewers.add(sview);
+ }
+ }
+ protected void setLoadingFinishedForNewStructureViewers()
+ {
+ if (newStructureViewers!=null)
+ {
+ for (AppJmol sview:newStructureViewers)
+ {
+ sview.jmb.setFinishedLoadingFromArchive(true);
+ }
+ newStructureViewers.clear();
+ newStructureViewers=null;
+ }
+ }
+
+ AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
+ Alignment al, JalviewModelSequence jms, Viewport view,
+ String uniqueSeqSetId, String viewId,
+ ArrayList autoAlan)
+ {
+ AlignFrame af = null;
+ af = new AlignFrame(al, view.getWidth(), view.getHeight(),
+ uniqueSeqSetId, viewId);
+
+ af.setFileName(file, "Jalview");
+
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ af.viewport.setSequenceColour(af.viewport.getAlignment()
+ .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
+ }
+
+ af.viewport.gatherViewsHere = view.getGatheredViews();
+
+ if (view.getSequenceSetId() != null)
+ {
+ jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) 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;
+ }
+ else
+ {
+ viewportsAdded.put(uniqueSeqSetId, af.viewport);
+ }
+ // TODO: check if this method can be called repeatedly without
+ // side-effects if alignpanel already registered.
+ PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
+ }
+ // apply Hidden regions to view.
+ if (hiddenSeqs != null)
+ {
+ for (int s = 0; s < JSEQ.length; s++)
+ {
+ jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
+
+ for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
+ {
+ hidden.addSequence(
+ al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
+ }
+ 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);
+ }
+
+ af.viewport.hideSequence(hseqs);
+
+ }
+ // recover view properties and display parameters
+ if (view.getViewName() != null)
+ {
+ af.viewport.viewName = view.getViewName();
+ af.setInitialTabVisible();
+ }
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+ view.getHeight());
+
+ af.viewport.setShowAnnotation(view.getShowAnnotation());
+ af.viewport.setAbovePIDThreshold(view.getPidSelected());
+
+ af.viewport.setColourText(view.getShowColourText());
+
+ 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.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.setShowUnconserved(view.hasShowUnconserved() ? view
+ .isShowUnconserved() : false);
+ af.viewport.setStartRes(view.getStartRes());
+ af.viewport.setStartSeq(view.getStartSeq());
+
+ ColourSchemeI cs = null;
+ // apply colourschemes
+ if (view.getBgColour() != null)
+ {
+ if (view.getBgColour().startsWith("ucs"))
+ {
+ 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());
+ }
+
+ // 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());
+ }
+
+ }
+ }
+ break;
+ }
+
+ }
}
}
else
@@ -1686,229 +3287,861 @@ public class Jalview2XML
if (cs != null)
{
cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.hconsensus);
+ cs.setConsensus(af.viewport.getSequenceConsensusHash());
+ }
+ }
+
+ af.viewport.setGlobalColourScheme(cs);
+ af.viewport.setColourAppliesToAllGroups(false);
+
+ if (view.getConservationSelected() && cs != null)
+ {
+ cs.setConservationInc(view.getConsThreshold());
+ }
+
+ af.changeColour(cs);
+
+ af.viewport.setColourAppliesToAllGroups(true);
+
+ if (view.getShowSequenceFeatures())
+ {
+ af.viewport.showSequenceFeatures = true;
+ }
+ if (view.hasCentreColumnLabels())
+ {
+ af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
+ }
+ if (view.hasIgnoreGapsinConsensus())
+ {
+ af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
+ null);
+ }
+ if (view.hasFollowHighlight())
+ {
+ af.viewport.followHighlight = view.getFollowHighlight();
+ }
+ if (view.hasFollowSelection())
+ {
+ af.viewport.followSelection = view.getFollowSelection();
+ }
+ if (view.hasShowConsensusHistogram())
+ {
+ af.viewport.setShowConsensusHistogram(view
+ .getShowConsensusHistogram());
+ }
+ else
+ {
+ af.viewport.setShowConsensusHistogram(true);
+ }
+ if (view.hasShowSequenceLogo())
+ {
+ af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
+ }
+ else
+ {
+ af.viewport.setShowSequenceLogo(false);
+ }
+ if (view.hasNormaliseSequenceLogo())
+ {
+ af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
+ }
+ if (view.hasShowDbRefTooltip())
+ {
+ af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
+ }
+ if (view.hasShowNPfeatureTooltip())
+ {
+ af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
+ }
+ if (view.hasShowGroupConsensus())
+ {
+ af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
+ }
+ else
+ {
+ af.viewport.setShowGroupConsensus(false);
+ }
+ if (view.hasShowGroupConservation())
+ {
+ af.viewport.setShowGroupConservation(view.getShowGroupConservation());
+ }
+ else
+ {
+ af.viewport.setShowGroupConservation(false);
+ }
+
+ // recover featre settings
+ if (jms.getFeatureSettings() != null)
+ {
+ af.viewport.featuresDisplayed = new Hashtable();
+ String[] renderOrder = new String[jms.getFeatureSettings()
+ .getSettingCount()];
+ for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+ {
+ Setting setting = jms.getFeatureSettings().getSetting(fs);
+ if (setting.hasMincolour())
+ {
+ GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
+ new java.awt.Color(setting.getMincolour()),
+ new java.awt.Color(setting.getColour()),
+ setting.getMin(), setting.getMax()) : new GraduatedColor(
+ new java.awt.Color(setting.getMincolour()),
+ new java.awt.Color(setting.getColour()), 0, 1);
+ if (setting.hasThreshold())
+ {
+ gc.setThresh(setting.getThreshold());
+ gc.setThreshType(setting.getThreshstate());
+ }
+ gc.setAutoScaled(true); // default
+ if (setting.hasAutoScale())
+ {
+ gc.setAutoScaled(setting.getAutoScale());
+ }
+ if (setting.hasColourByLabel())
+ {
+ gc.setColourByLabel(setting.getColourByLabel());
+ }
+ // and put in the feature colour table.
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ setting.getType(), gc);
+ }
+ else
+ {
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ 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());
+ else
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+ setting.getType(),
+ fs / jms.getFeatureSettings().getSettingCount());
+ if (setting.getDisplay())
+ {
+ af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+ setting.getColour()));
+ }
+ }
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+ Hashtable fgtable;
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = 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()));
+ }
+ }
+
+ if (view.getHiddenColumnsCount() > 0)
+ {
+ for (int c = 0; c < view.getHiddenColumnsCount(); c++)
+ {
+ af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
+ .getHiddenColumns(c).getEnd() // +1
+ );
+ }
+ }
+ if (view.getCalcIdParam() != null)
+ {
+ for (CalcIdParam calcIdParam : view.getCalcIdParam())
+ {
+ if (calcIdParam != null)
+ {
+ if (recoverCalcIdParam(calcIdParam, af.viewport))
+ {
+ }
+ else
+ {
+ warn("Couldn't recover parameters for "
+ + calcIdParam.getCalcId());
+ }
+ }
+ }
+ }
+ af.setMenusFromViewport(af.viewport);
+ // TODO: we don't need to do this if the viewport is aready visible.
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+ view.getHeight());
+ af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
+ reorderAutoannotation(af, al, autoAlan);
+ return af;
+ }
+
+ private void reorderAutoannotation(AlignFrame af, Alignment al,
+ ArrayList autoAlan)
+ {
+ // copy over visualization settings for autocalculated annotation in the
+ // view
+ if (al.getAlignmentAnnotation() != null)
+ {
+ /**
+ * Kludge for magic autoannotation names (see JAL-811)
+ */
+ String[] magicNames = new String[]
+ { "Consensus", "Quality", "Conservation" };
+ JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
+ Hashtable visan = new Hashtable();
+ for (String nm : magicNames)
+ {
+ visan.put(nm, nullAnnot);
+ }
+ for (JvAnnotRow auan : autoAlan)
+ {
+ visan.put(auan.template.label
+ + (auan.template.getCalcId() == null ? "" : "\t"
+ + auan.template.getCalcId()), auan);
+ }
+ int hSize = al.getAlignmentAnnotation().length;
+ ArrayList reorder = new ArrayList();
+ // work through any autoCalculated annotation already on the view
+ // removing it if it should be placed in a different location on the
+ // annotation panel.
+ List remains = new ArrayList(visan.keySet());
+ for (int h = 0; h < hSize; h++)
+ {
+ jalview.datamodel.AlignmentAnnotation jalan = al
+ .getAlignmentAnnotation()[h];
+ if (jalan.autoCalculated)
+ {
+ String k;
+ JvAnnotRow valan = visan.get(k = jalan.label);
+ if (jalan.getCalcId() != null)
+ {
+ valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
+ }
+
+ if (valan != null)
+ {
+ // delete the auto calculated row from the alignment
+ al.deleteAnnotation(jalan, false);
+ remains.remove(k);
+ hSize--;
+ h--;
+ if (valan != nullAnnot)
+ {
+ if (jalan != valan.template)
+ {
+ // newly created autoannotation row instance
+ // so keep a reference to the visible annotation row
+ // and copy over all relevant attributes
+ if (valan.template.graphHeight >= 0)
+
+ {
+ jalan.graphHeight = valan.template.graphHeight;
+ }
+ jalan.visible = valan.template.visible;
+ }
+ reorder.add(new JvAnnotRow(valan.order, jalan));
+ }
+ }
+ }
+ }
+ // Add any (possibly stale) autocalculated rows that were not appended to
+ // the view during construction
+ for (String other : remains)
+ {
+ JvAnnotRow othera = visan.get(other);
+ if (othera != nullAnnot && othera.template.getCalcId() != null
+ && othera.template.getCalcId().length() > 0)
+ {
+ reorder.add(othera);
+ }
+ }
+ // now put the automatic annotation in its correct place
+ int s = 0, srt[] = new int[reorder.size()];
+ JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
+ for (JvAnnotRow jvar : reorder)
+ {
+ rws[s] = jvar;
+ srt[s++] = jvar.order;
+ }
+ reorder.clear();
+ jalview.util.QuickSort.sort(srt, rws);
+ // and re-insert the annotation at its correct position
+ for (JvAnnotRow jvar : rws)
+ {
+ al.addAnnotation(jvar.template, jvar.order);
+ }
+ af.alignPanel.adjustAnnotationHeight();
+ }
+ }
+
+ Hashtable skipList = null;
+
+ /**
+ * TODO remove this method
+ *
+ * @param view
+ * @return AlignFrame bound to sequenceSetId from view, if one exists. private
+ * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
+ * throw new Error("Implementation Error. No skipList defined for this
+ * Jalview2XML instance."); } return (AlignFrame)
+ * skipList.get(view.getSequenceSetId()); }
+ */
+
+ /**
+ * Check if the Jalview view contained in object should be skipped or not.
+ *
+ * @param object
+ * @return true if view's sequenceSetId is a key in skipList
+ */
+ private boolean skipViewport(JalviewModel object)
+ {
+ if (skipList == null)
+ {
+ return false;
+ }
+ String id;
+ if (skipList.containsKey(id = object.getJalviewModelSequence()
+ .getViewport()[0].getSequenceSetId()))
+ {
+ if (Cache.log != null && Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Skipping seuqence set id " + id);
}
+ return true;
}
+ return false;
+ }
- af.viewport.setGlobalColourScheme(cs);
- af.viewport.setColourAppliesToAllGroups(false);
-
- if (view.getConservationSelected() && cs != null)
+ public void AddToSkipList(AlignFrame af)
+ {
+ if (skipList == null)
{
- cs.setConservationInc(view.getConsThreshold());
+ skipList = new Hashtable();
}
+ skipList.put(af.getViewport().getSequenceSetId(), af);
+ }
- af.changeColour(cs);
+ public void clearSkipList()
+ {
+ if (skipList != null)
+ {
+ skipList.clear();
+ skipList = null;
+ }
+ }
- af.viewport.setColourAppliesToAllGroups(true);
+ private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
+ {
+ jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
+ Vector dseqs = null;
+ if (ds == null)
+ {
+ // create a list of new dataset sequences
+ dseqs = new Vector();
+ }
+ for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
+ {
+ Sequence vamsasSeq = vamsasSet.getSequence(i);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
+ }
+ // create a new dataset
+ if (ds == null)
+ {
+ SequenceI[] dsseqs = new SequenceI[dseqs.size()];
+ dseqs.copyInto(dsseqs);
+ ds = new jalview.datamodel.Alignment(dsseqs);
+ debug("Created new dataset " + vamsasSet.getDatasetId()
+ + " for alignment " + System.identityHashCode(al));
+ addDatasetRef(vamsasSet.getDatasetId(), ds);
+ }
+ // set the dataset for the newly imported alignment.
+ if (al.getDataset() == null)
+ {
+ al.setDataset(ds);
+ }
+ }
- if (view.getShowSequenceFeatures())
+ /**
+ *
+ * @param vamsasSeq
+ * sequence definition to create/merge dataset sequence for
+ * @param ds
+ * dataset alignment
+ * @param dseqs
+ * vector to add new dataset sequence to
+ */
+ private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
+ AlignmentI ds, Vector dseqs)
+ {
+ // 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;
+ if (sq != null && sq.getDatasetSequence() != null)
{
- af.viewport.showSequenceFeatures = true;
+ dsq = sq.getDatasetSequence();
}
- if (jms.getFeatureSettings() != null)
+ String sqid = vamsasSeq.getDsseqid();
+ if (dsq == null)
{
- af.viewport.featuresDisplayed = new Hashtable();
- String[] renderOrder = new String[jms.getFeatureSettings().
- getSettingCount()];
- for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+ // need to create or add a new dataset sequence reference to this sequence
+ if (sqid != null)
{
- Setting setting = jms.getFeatureSettings().getSetting(fs);
-
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(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());
+ dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
+ }
+ // check again
+ if (dsq == null)
+ {
+ // make a new dataset sequence
+ dsq = sq.createDatasetSequence();
+ if (sqid == null)
+ {
+ // make up a new dataset reference for this sequence
+ sqid = seqHash(dsq);
+ }
+ dsq.setVamsasId(uniqueSetSuffix + sqid);
+ seqRefIds.put(sqid, dsq);
+ if (ds == null)
+ {
+ if (dseqs != null)
+ {
+ dseqs.addElement(dsq);
+ }
+ }
else
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), fs/jms.getFeatureSettings().getSettingCount());
- if (setting.getDisplay())
{
- af.viewport.featuresDisplayed.put(
- setting.getType(), new Integer(setting.getColour()));
+ ds.addSequence(dsq);
}
}
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
- renderOrder;
- Hashtable fgtable;
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable=new Hashtable();
- for (int gs=0;gs 0)
+ // TODO: refactor this as a merge dataset sequence function
+ // now check that sq (the dataset sequence) sequence really is the union of
+ // all references to it
+ // boolean pre = sq.getStart() < dsq.getStart();
+ // boolean post = sq.getEnd() > dsq.getEnd();
+ // if (pre || post)
+ if (sq != dsq)
{
- for (int c = 0; c < view.getHiddenColumnsCount(); c++)
+ StringBuffer sb = new StringBuffer();
+ String newres = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, sq.getSequenceAsString());
+ if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
+ && newres.length() > dsq.getLength())
{
- af.viewport.hideColumns(
- view.getHiddenColumns(c).getStart(),
- view.getHiddenColumns(c).getEnd() //+1
- );
+ // Update with the longer sequence.
+ synchronized (dsq)
+ {
+ /*
+ * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
+ * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
+ * sb.append(newres.substring(newres.length() - sq.getEnd() -
+ * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
+ */
+ dsq.setSequence(sb.toString());
+ }
+ // 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"); // ("
+ // + (pre ? "prepended" : "") + " "
+ // + (post ? "appended" : ""));
}
}
+ }
- af.setMenusFromViewport(af.viewport);
+ java.util.Hashtable datasetIds = null;
- Desktop.addInternalFrame(af, view.getTitle(),
- view.getWidth(), view.getHeight());
+ java.util.IdentityHashMap dataset2Ids = null;
- //LOAD TREES
- ///////////////////////////////////////
- if (loadTreesAndStructures && jms.getTreeCount() > 0)
+ private Alignment getDatasetFor(String datasetId)
+ {
+ if (datasetIds == null)
{
- try
- {
- for (int t = 0; t < jms.getTreeCount(); t++)
- {
-
- Tree tree = jms.getTree(t);
-
- TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
- tree.getNewick()), tree.getTitle(),
- tree.getWidth(), tree.getHeight(),
- tree.getXpos(), tree.getYpos());
-
- tp.fitToWindow.setState(tree.getFitToWindow());
- tp.fitToWindow_actionPerformed(null);
-
- if (tree.getFontName() != null)
- {
- tp.setTreeFont(new java.awt.Font(tree.getFontName(),
- tree.getFontStyle(),
- tree.getFontSize()));
- }
- else
- {
- tp.setTreeFont(new java.awt.Font(view.getFontName(),
- view.getFontStyle(),
- tree.getFontSize()));
- }
-
- tp.showPlaceholders(tree.getMarkUnlinked());
- tp.showBootstrap(tree.getShowBootstrap());
- tp.showDistances(tree.getShowDistances());
-
- tp.treeCanvas.threshold = tree.getThreshold();
+ datasetIds = new Hashtable();
+ return null;
+ }
+ if (datasetIds.containsKey(datasetId))
+ {
+ return (Alignment) datasetIds.get(datasetId);
+ }
+ return null;
+ }
- if (tree.getCurrentTree())
- {
- af.viewport.setCurrentTree(tp.getTree());
- }
- }
+ private void addDatasetRef(String datasetId, Alignment dataset)
+ {
+ if (datasetIds == null)
+ {
+ datasetIds = new Hashtable();
+ }
+ datasetIds.put(datasetId, dataset);
+ }
+ /**
+ * make a new dataset ID for this jalview dataset alignment
+ *
+ * @param dataset
+ * @return
+ */
+ private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
+ {
+ if (dataset.getDataset() != null)
+ {
+ warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
+ }
+ String datasetId = makeHashCode(dataset, null);
+ if (datasetId == null)
+ {
+ // make a new datasetId and record it
+ if (dataset2Ids == null)
+ {
+ dataset2Ids = new IdentityHashMap();
}
- catch (Exception ex)
+ else
{
- ex.printStackTrace();
+ datasetId = (String) dataset2Ids.get(dataset);
+ }
+ if (datasetId == null)
+ {
+ datasetId = "ds" + dataset2Ids.size() + 1;
+ dataset2Ids.put(dataset, datasetId);
}
}
+ return datasetId;
+ }
- ////LOAD STRUCTURES
- if(loadTreesAndStructures)
+ private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
+ {
+ for (int d = 0; d < sequence.getDBRefCount(); d++)
{
- for (int i = 0; i < JSEQ.length; i++)
+ DBRef dr = sequence.getDBRef(d);
+ jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
+ sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
+ .getVersion(), sequence.getDBRef(d).getAccessionId());
+ if (dr.getMapping() != null)
{
- if (JSEQ[i].getPdbidsCount() > 0)
- {
- Pdbids[] ids = JSEQ[i].getPdbids();
- for (int p = 0; p < ids.length; p++)
- {
- for (int s = 0; s < ids[p].getStructureStateCount(); s++)
- {
- jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
-
- jpdb.setFile(loadPDBFile(ids[p].getFile(), 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();
-
- java.awt.Component comp = Desktop.desktop.getComponentAt(x, y);
-
- String pdbFile = loadPDBFile(file, ids[p].getId());
-
- jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
- {
- al.getSequenceAt(i)};
-
- if (comp == null ||
- (comp.getWidth() != width && comp.getHeight() != height))
- {
- String state = ids[p].getStructureState(s).getContent();
-
- StringBuffer newFileLoc = new StringBuffer(state.substring(0,
- state.indexOf("\"", state.indexOf("load")) + 1));
-
- newFileLoc.append(jpdb.getFile());
- newFileLoc.append(state.substring(
- state.indexOf("\"", state.indexOf("load \"") + 6)));
+ entry.setMap(addMapping(dr.getMapping()));
+ }
+ datasetSequence.addDBRef(entry);
+ }
+ }
- new AppJMol(pdbFile,
- ids[p].getId(),
- seq,
- af.alignPanel,
- newFileLoc.toString(),
- new java.awt.Rectangle(x, y, width, height));
+ private jalview.datamodel.Mapping addMapping(Mapping m)
+ {
+ SequenceI dsto = null;
+ // Mapping m = dr.getMapping();
+ int fr[] = new int[m.getMapListFromCount() * 2];
+ Enumeration f = m.enumerateMapListFrom();
+ for (int _i = 0; f.hasMoreElements(); _i += 2)
+ {
+ MapListFrom mf = (MapListFrom) f.nextElement();
+ fr[_i] = mf.getStart();
+ fr[_i + 1] = mf.getEnd();
+ }
+ int fto[] = new int[m.getMapListToCount() * 2];
+ f = m.enumerateMapListTo();
+ for (int _i = 0; f.hasMoreElements(); _i += 2)
+ {
+ MapListTo mf = (MapListTo) f.nextElement();
+ fto[_i] = mf.getStart();
+ fto[_i + 1] = mf.getEnd();
+ }
+ jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
+ fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
+ if (m.getMappingChoice() != null)
+ {
+ MappingChoice mc = m.getMappingChoice();
+ if (mc.getDseqFor() != null)
+ {
+ String dsfor = "" + mc.getDseqFor();
+ if (seqRefIds.containsKey(dsfor))
+ {
+ /**
+ * recover from hash
+ */
+ jmap.setTo((SequenceI) seqRefIds.get(dsfor));
+ }
+ else
+ {
+ frefedSequence.add(new Object[]
+ { dsfor, jmap });
+ }
+ }
+ else
+ {
+ /**
+ * local sequence definition
+ */
+ Sequence ms = mc.getSequence();
+ jalview.datamodel.Sequence djs = null;
+ String sqid = ms.getDsseqid();
+ if (sqid != null && sqid.length() > 0)
+ {
+ /*
+ * recover dataset sequence
+ */
+ djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
+ }
+ else
+ {
+ System.err
+ .println("Warning - making up dataset sequence id for DbRef sequence map reference");
+ sqid = ((Object) ms).toString(); // make up a new hascode for
+ // undefined dataset sequence hash
+ // (unlikely to happen)
+ }
- }
- else if(comp!=null)
- {
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, pdbFile,
- jalview.io.AppletFormatAdapter.FILE);
+ if (djs == null)
+ {
+ /**
+ * make a new dataset sequence and add it to refIds hash
+ */
+ djs = new jalview.datamodel.Sequence(ms.getName(),
+ ms.getSequence());
+ djs.setStart(jmap.getMap().getToLowest());
+ djs.setEnd(jmap.getMap().getToHighest());
+ djs.setVamsasId(uniqueSetSuffix + sqid);
+ jmap.setTo(djs);
+ seqRefIds.put(sqid, djs);
- ( (AppJMol) comp).addSequence(seq);
- }
- }
- }
}
+ jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+ addDBRefs(djs, ms);
+
}
}
+ return (jmap);
- return af;
}
public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
- boolean keepSeqRefs)
+ boolean keepSeqRefs)
{
- jalview.schemabinding.version2.JalviewModel jm
- = SaveState(ap, null, null, null);
+ initSeqRefs();
+ jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
+ null);
if (!keepSeqRefs)
{
- seqRefIds.clear();
+ clearSeqRefs();
jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
}
else
{
uniqueSetSuffix = "";
+ jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
+ // overwrite the
+ // view we just
+ // copied
+ }
+ if (this.frefedSequence == null)
+ {
+ frefedSequence = new Vector();
}
viewportsAdded = new Hashtable();
- AlignFrame af = LoadFromObject(jm, null, false);
+ AlignFrame af = LoadFromObject(jm, null, false, null);
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
- /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
+ /*
+ * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
+ * i