import javax.swing.*;
import org.exolab.castor.xml.*;
+
+import uk.ac.vamsas.objects.utils.MapList;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
import jalview.schemes.*;
import jalview.structure.StructureSelectionManager;
/**
- * 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 $Revision$
public class Jalview2XML
{
- Hashtable seqRefIds;
+ Hashtable seqRefIds = null;
+
+ Vector frefedSequence = null;
+
+ 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
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
+ + ref[1].getClass() + " type objects.");
+ }
+ frefedSequence.remove(r);
+ rSize--;
+ }
+ else
+ {
+ r++;
+ }
+ }
+ else
+ {
+ frefedSequence.remove(r);
+ rSize--;
+ }
+ }
+ }
+ }
/**
* This maintains a list of viewports, the key being the
Hashtable annotationIds = new Hashtable();
String uniqueSetSuffix = "";
+
/**
* List of pdbfiles added to Jar
*/
//NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
////////////////////////////////////////////////////
PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
+ "UTF-8"));
Vector shortNames = new Vector();
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;
{
if (shortName.endsWith("_" + (count - 1)))
{
- shortName = shortName.substring(0,
- shortName.lastIndexOf("_"));
+ shortName = shortName
+ .substring(0, shortName.lastIndexOf("_"));
}
shortName = shortName.concat("_" + count);
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);
- SaveState(apanel,
- apSize == 1 ? shortName : ap + shortName,
- jout, out);
+ SaveState(apanel, apSize == 1 ? shortName : ap + shortName,
+ jout, out);
}
}
}
out.close();
jout.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
+ //TODO: inform user of the problem - they need to know if their data was not saved !
ex.printStackTrace();
}
}
// USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
public boolean SaveAlignment(AlignFrame af, String jarFile,
- String fileName)
+ String fileName)
{
try
{
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
+ "UTF-8"));
for (ap = 0; ap < apSize; ap++)
{
- AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap);
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
+ .elementAt(ap);
- SaveState(apanel,
- apSize == 1 ? fileName : fileName + ap,
- jout, out);
+ SaveState(apanel, apSize == 1 ? fileName : fileName + ap, jout, out);
}
out.close();
jout.close();
return true;
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
return false;
* @param jout DOCUMENT ME!
* @param out DOCUMENT ME!
*/
- public JalviewModel SaveState(AlignmentPanel ap,
- String fileName,
- JarOutputStream jout,
- PrintWriter out)
+ public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+ JarOutputStream jout, PrintWriter out)
{
if (seqRefIds == null)
{
vamsasSet.setGapChar(jal.getGapCharacter() + "");
- if(jal.getProperties()!=null)
+ if (jal.getDataset() != null)
+ {
+ // dataset id is the dataset's hashcode
+ vamsasSet.setDatasetId(jal.getDataset().hashCode() + "");
+ }
+ if (jal.getProperties() != null)
{
Enumeration en = jal.getProperties().keys();
- while(en.hasMoreElements())
+ while (en.hasMoreElements())
{
String key = en.nextElement().toString();
SequenceSetProperties ssp = new SequenceSetProperties();
}
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));
}
jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
+ && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
{
- jalview.datamodel.SequenceI[] reps =
- ( (jalview.datamodel.SequenceGroup)
- av.hiddenRepSequences.get(
- jal.getSequenceAt(i))).getSequencesInOrder(jal);
+ jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
+ .get(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]));
}
}
}
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)
{
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);
}
}
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;
+ AppJmol jmol;
//This must have been loaded, is it still visible?
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int f = frames.length - 1; f > -1; f--)
{
- if (frames[f] instanceof AppJMol)
+ if (frames[f] instanceof AppJmol)
{
- jmol = (AppJMol) frames[f];
+ jmol = (AppJmol) frames[f];
if (!jmol.pdbentry.getId().equals(entry.getId()))
continue;
-
StructureState state = new StructureState();
state.setVisible(true);
state.setXpos(jmol.getX());
state.setHeight(jmol.getHeight());
String statestring = jmol.viewer.getStateInfo();
- if(state!=null)
+ if (state != null)
{
state.setContent(statestring.replaceAll("\n", ""));
}
}
}
-
if (entry.getFile() != null)
{
pdb.setFile(entry.getFile());
File file = new File(entry.getFile());
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);
jout.closeEntry();
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
- ex.printStackTrace();
+ ex.printStackTrace();
}
}
{
jal = av.alignment;
}
+ // 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; i++)
+ {
+ Alcodon cmap = new Alcodon();
+ 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("" + dnas[m].hashCode());
+ alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
+ false));
+ alc.addAlcodMap(alcmap);
+ }
+ }
+ }
+ }
//SAVE TREES
///////////////////////////////////
{
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);
//SAVE ANNOTATIONS
if (jal.getAlignmentAnnotation() != null)
{
- jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
+ jalview.datamodel.AlignmentAnnotation[] aa = jal
+ .getAlignmentAnnotation();
for (int i = 0; i < aa.length; i++)
{
an.setId(aa[i].annotationId);
- if (aa[i] == av.quality ||
- aa[i] == av.conservation ||
- aa[i] == av.consensus)
+ if (aa[i] == av.quality || aa[i] == av.conservation
+ || aa[i] == av.consensus)
{
an.setLabel(aa[i].label);
an.setGraph(true);
continue;
}
+ an.setVisible(aa[i].visible);
+
an.setDescription(aa[i].description);
if (aa[i].sequenceRef != null)
an.setScore(aa[i].getScore());
}
AnnotationElement ae;
- if (aa[i].annotations!=null)
+ if (aa[i].annotations != null)
{
an.setScoreOnly(false);
for (int a = 0; a < aa[i].annotations.length; a++)
ae = new AnnotationElement();
if (aa[i].annotations[a].description != null)
ae.setDescription(aa[i].annotations[a].description);
- if(aa[i].annotations[a].displayCharacter!=null)
+ if (aa[i].annotations[a].displayCharacter != null)
ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
if (!Float.isNaN(aa[i].annotations[a].value))
ae.setPosition(a);
if (aa[i].annotations[a].secondaryStructure != ' '
- && aa[i].annotations[a].secondaryStructure != '\0')
- ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
- + "");
+ && 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)
+ 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);
}
- } else {
+ }
+ else
+ {
an.setScoreOnly(true);
}
vamsasSet.addAnnotation(an);
{
groups[i] = new JGroup();
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
- jal.getGroups()
- .elementAt(i);
+ 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 (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());
for (int s = 0; s < sg.getSize(); s++)
{
- jalview.datamodel.Sequence seq =
- (jalview.datamodel.Sequence) sg.getSequenceAt(s);
+ jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
+ .getSequenceAt(s);
groups[i].addSeq(seq.hashCode());
}
}
view.setViewName(av.viewName);
view.setGatheredViews(av.gatherViewsHere);
-
-
if (ap.av.explodedPosition != null)
{
view.setXpos(av.explodedPosition.x);
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());
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());
}
else
{
- view.setBgColour(ColourSchemeProperty.getColourName(
- av.getGlobalColourScheme()));
+ view.setBgColour(ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
}
ColourSchemeI cs = av.getGlobalColourScheme();
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++)
{
Setting setting = new Setting();
setting.setType(renderOrder[ro]);
- 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.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(renderOrder[ro]).getRGB());
+
+ setting.setDisplay(av.featuresDisplayed
+ .containsKey(renderOrder[ro]));
+ float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
+ renderOrder[ro]);
+ if (rorder > -1)
+ {
setting.setOrder(rorder);
}
fs.addSetting(setting);
}
//Make sure we save none displayed feature settings
- Enumeration en =
- ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+ Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+ .keys();
while (en.hasMoreElements())
{
String key = en.nextElement().toString();
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);
}
settingsAdded.addElement(key);
}
en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
- Vector groupsAdded=new Vector();
+ Vector groupsAdded = new Vector();
while (en.hasMoreElements())
{
String grp = en.nextElement().toString();
}
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);
}
{
for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
- elementAt(c);
+ int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+ .elementAt(c);
HiddenColumns hc = new HiddenColumns();
hc.setStart(region[0]);
hc.setEnd(region[1]);
jout.putNextEntry(entry);
object.marshal(out);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
return object;
}
+ private Sequence createVamsasSequence(int id, SequenceI jds)
+ {
+ return createVamsasSequence(true, id, jds, null);
+ }
+
+ private Sequence createVamsasSequence(boolean recurse, int 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(jds.getDatasetSequence().hashCode() + "");
+ if (jds.getDatasetSequence().getDBRef() != null)
+ {
+ dbrefs = jds.getDatasetSequence().getDBRef();
+ }
+ }
+ else
+ {
+ dbrefs = jds.getDBRef();
+ }
+ if (jds.getDBRef() != 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, jmp.getTo()
+ .hashCode(), jmp.getTo(), jds));
+ }
+ else
+ {
+ long jmpid = 0;
+ SequenceI ps = null;
+ if (parentseq != jmp.getTo()
+ && parentseq.getDatasetSequence() != jmp.getTo())
+ {
+ // chaining dbref rather than a handshaking one
+ jmpid = (ps = jmp.getTo()).hashCode();
+ }
+ else
+ {
+ jmpid = (ps = parentseq).hashCode();
+ }
+ 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;
if (!userColours.contains(ucs))
{
userColours.add(ucs);
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);
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);
}
jalview.schemes.UserColourScheme GetUserColourScheme(
- JalviewModelSequence jms, String id)
+ JalviewModelSequence jms, String id)
{
UserColours[] uc = jms.getUserColours();
UserColours colours = null;
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);
}
seqRefIds = new Hashtable();
viewportsAdded = new Hashtable();
-
+ frefedSequence = new Vector();
Hashtable gatherToThisFrame = new Hashtable();
+ String errorMessage = null;
+
try
{
//UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
//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()
- {
- public void run()
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't locate " + file,
- "URL not found",
- JOptionPane.WARNING_MESSAGE);
- }
- });
- }
- catch (Exception ex)
+ 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)
{
//Is Version 1 Jar file?
af = new Jalview2XML_V1().LoadJalviewAlign(file);
}
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");
}
if (Desktop.instance != null)
}
Enumeration en = gatherToThisFrame.elements();
- while(en.hasMoreElements())
+ while (en.hasMoreElements())
+ {
+ Desktop.instance.gatherViews((AlignFrame) en.nextElement());
+ }
+
+ if (errorMessage != null)
{
- Desktop.instance.gatherViews(
- (AlignFrame) en.nextElement());
+ final String finalErrorMessage = errorMessage;
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ finalErrorMessage, "Error loading Jalview file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
}
return af;
}
Hashtable alreadyLoadedPDB;
+
String loadPDBFile(String file, String pdbId)
{
if (alreadyLoadedPDB == null)
do
{
entry = jin.getNextJarEntry();
- }
- while (!entry.getName().equals(pdbId));
+ } while (!entry.getName().equals(pdbId));
BufferedReader in = new BufferedReader(new InputStreamReader(jin));
File outFile = File.createTempFile("jalview_pdb", ".txt");
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
String data;
- while ( (data = in.readLine()) != null)
+ while ((data = in.readLine()) != null)
{
out.println(data);
}
alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
return outFile.getAbsolutePath();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
return null;
}
- AlignFrame LoadFromObject(JalviewModel object,
- String file,
- boolean loadTreesAndStructures)
+ AlignFrame LoadFromObject(JalviewModel object, String file,
+ boolean loadTreesAndStructures)
{
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
Sequence[] vamsasSeq = vamsasSet.getSequence();
if (seqRefIds.get(seqId) != null)
{
- tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
multipleView = true;
}
else
{
jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
- vamsasSeq[i].getSequence());
+ vamsasSeq[i].getSequence());
jseq.setDescription(vamsasSeq[i].getDescription());
jseq.setStart(JSEQ[i].getStart());
jseq.setEnd(JSEQ[i].getEnd());
+ jseq.setVamsasId(uniqueSetSuffix + seqId);
seqRefIds.put(vamsasSeq[i].getId(), jseq);
tmpseqs.add(jseq);
}
hiddenSeqs = new Vector();
}
- hiddenSeqs.addElement(
- (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
+ .get(seqId));
}
}
- ///SequenceFeatures are added to the DatasetSequence,
- // so we must create the dataset before loading features
+ ///
+ // Create the alignment object from the sequence set
/////////////////////////////////
-
-
- jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
- tmpseqs.size()];
+ jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
+ .size()];
tmpseqs.toArray(orderedSeqs);
- jalview.datamodel.Alignment al =
- new jalview.datamodel.Alignment(orderedSeqs);
+ jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
+ orderedSeqs);
- for(int i=0; i<vamsasSet.getSequenceSetPropertiesCount(); i++ )
+ /// Add the alignment properties
+ for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
{
SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
al.setProperty(ssp.getKey(), ssp.getValue());
}
-
- al.setDataset(null);
+ ///
+ // 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)
{
for (int i = 0; i < vamsasSeq.length; i++)
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++)
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)
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
}
}
- if (vamsasSeq[i].getDBRefCount() > 0)
+ }
+ }
+
+ /////////////////////////////////
+ // LOAD SEQUENCE MAPPINGS
+ if (vamsasSet.getAlcodonFrameCount() > 0)
+ {
+ 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);
+ 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();
+ }
+ }
+ 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
+ // attach to dna sequence reference.
+ if (dnaseq != null)
+ {
+ if (maps[m].getMapping() != null)
+ {
+ jalview.datamodel.Mapping mapping = addMapping(maps[m]
+ .getMapping());
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ }
}
-
}
+ al.addCodonFrame(cf);
}
+
}
- /////////////////////////////////
//////////////////////////////////
//LOAD ANNOTATIONS
- boolean hideQuality = true,
- hideConservation = true,
- hideConsensus = true;
+ boolean hideQuality = true, hideConservation = true, hideConsensus = true;
if (vamsasSet.getAnnotationCount() > 0)
{
}
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());
+ if (an[i].hasVisible())
+ jda.visible = an[i].getVisible();
+
+ al.addAnnotation(jda);
continue;
}
if (!an[i].getScoreOnly())
{
- anot = new jalview.datamodel.Annotation[
- al.getWidth()];
+ anot = new jalview.datamodel.Annotation[al.getWidth()];
for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
{
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+ if (ae[aa].getPosition() >= anot.length)
+ continue;
- ae[aa].getDisplayCharacter(),
- ae[aa].getDescription(),
- (ae[aa].getSecondaryStructure()==null || ae[aa].getSecondaryStructure().length() == 0) ? ' ' :
- ae[aa].getSecondaryStructure().charAt(0),
- ae[aa].getValue()
+ anot[ae[aa].getPosition()] = 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()
+ );
- anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
- getColour());
+ anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
+ .getColour());
}
}
jalview.datamodel.AlignmentAnnotation jaa = null;
if (an[i].getGraph())
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot, 0, 0,
- an[i].getGraphType());
+ an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
jaa.graphGroup = an[i].getGraphGroup();
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())));
}
else
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot);
+ an[i].getDescription(), anot);
}
if (an[i].getId() != null)
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);
+ }
}
if (an[i].hasScore())
{
jaa.setScore(an[i].getScore());
}
+
+ if (an[i].hasVisible())
+ jaa.visible = an[i].getVisible();
+
al.addAnnotation(jaa);
}
}
}
else
{
- cs = ColourSchemeProperty.getColour(al,
- groups[i].getColour());
+ cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
}
if (cs != null)
for (int s = 0; s < groups[i].getSeqCount(); s++)
{
String seqId = groups[i].getSeq(s) + "";
- jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
- seqRefIds.get(seqId);
+ jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
+ .get(seqId);
if (ts != null)
{
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());
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);
/////////////////////////////////
// LOAD VIEWPORT
- AlignFrame af = new AlignFrame(al,
- view.getWidth(),
- view.getHeight());
+ 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()));
+ 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
if (view.getSequenceSetId() != null)
{
- jalview.gui.AlignViewport av =
- (jalview.gui.AlignViewport)
- viewportsAdded.get(uniqueSeqSetId);
+ jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
+ .get(uniqueSeqSetId);
af.viewport.sequenceSetID = uniqueSeqSetId;
if (av != null)
{
for (int s = 0; s < JSEQ.length; s++)
{
- jalview.datamodel.SequenceGroup hidden =
- new jalview.datamodel.SequenceGroup();
+ 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
- );
+ 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()];
+ jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
+ .size()];
for (int s = 0; s < hiddenSeqs.size(); s++)
{
}
- if ( (hideConsensus || hideQuality || hideConservation)
- && al.getAlignmentAnnotation() != null)
+ if ((hideConsensus || hideQuality || hideConservation)
+ && al.getAlignmentAnnotation() != null)
{
int hSize = al.getAlignmentAnnotation().length;
for (int h = 0; h < hSize; h++)
{
- if (
- (hideConsensus &&
- al.getAlignmentAnnotation()[h].label.equals("Consensus"))
- ||
- (hideQuality &&
- al.getAlignmentAnnotation()[h].label.equals("Quality"))
- ||
- (hideConservation &&
- al.getAlignmentAnnotation()[h].label.equals("Conservation")))
+ if ((hideConsensus && al.getAlignmentAnnotation()[h].label
+ .equals("Consensus"))
+ || (hideQuality && al.getAlignmentAnnotation()[h].label
+ .equals("Quality"))
+ || (hideConservation && al.getAlignmentAnnotation()[h].label
+ .equals("Conservation")))
{
al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
hSize--;
af.viewport.viewName = view.getViewName();
af.setInitialTabVisible();
}
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
- view.getHeight());
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
+ .getHeight());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
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.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());
else if (view.getBgColour().startsWith("Annotation"))
{
//int find annotation
- for (int i = 0;
- i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
- equals(view.getAnnotationColours().getAnnotation()))
+ if (af.viewport.alignment.getAlignmentAnnotation()[i].label
+ .equals(view.getAnnotationColours().getAnnotation()))
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i].
- getThreshold() == null)
+ if (af.viewport.alignment.getAlignmentAnnotation()[i]
+ .getThreshold() == null)
{
- af.viewport.alignment.getAlignmentAnnotation()[i].
- setThreshold(
- new jalview.datamodel.GraphLine(
- view.getAnnotationColours().getThreshold(),
- "Threshold", java.awt.Color.black)
+ af.viewport.alignment.getAlignmentAnnotation()[i]
+ .setThreshold(new jalview.datamodel.GraphLine(view
+ .getAnnotationColours().getThreshold(),
+ "Threshold", java.awt.Color.black)
- );
+ );
}
- if (view.getAnnotationColours().getColourScheme().equals(
- "None"))
+ 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());
+ 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"))
+ else if (view.getAnnotationColours().getColourScheme()
+ .startsWith("ucs"))
{
- cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- GetUserColourScheme(jms, view.getAnnotationColours().
- getColourScheme()),
- view.getAnnotationColours().getAboveThreshold()
- );
+ 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()
- );
+ cs = new AnnotationColourGradient(af.viewport.alignment
+ .getAlignmentAnnotation()[i], ColourSchemeProperty
+ .getColour(al, view.getAnnotationColours()
+ .getColourScheme()), view
+ .getAnnotationColours().getAboveThreshold());
}
// Also use these settings for all the groups
{
for (int g = 0; g < al.getGroups().size(); g++)
{
- jalview.datamodel.SequenceGroup sg
- = (jalview.datamodel.SequenceGroup) al.getGroups().
- elementAt(g);
+ jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
+ .getGroups().elementAt(g);
if (sg.cs == null)
{
else*/
{
sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- sg.cs,
- view.getAnnotationColours().getAboveThreshold()
- );
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ sg.cs, view.getAnnotationColours()
+ .getAboveThreshold());
}
}
if (jms.getFeatureSettings() != null)
{
af.viewport.featuresDisplayed = new Hashtable();
- String[] renderOrder = new String[jms.getFeatureSettings().
- getSettingCount()];
+ String[] renderOrder = new String[jms.getFeatureSettings()
+ .getSettingCount()];
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
- getType(),
- new java.awt.Color(setting.getColour()));
+ 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());
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+ setting.getType(), setting.getOrder());
else
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), fs/jms.getFeatureSettings().getSettingCount());
+ 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.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+ setting.getColour()));
}
}
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
- renderOrder;
+ 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++)
+ 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()));
{
for (int c = 0; c < view.getHiddenColumnsCount(); c++)
{
- af.viewport.hideColumns(
- view.getHiddenColumns(c).getStart(),
- view.getHiddenColumns(c).getEnd() //+1
- );
+ af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
+ .getHiddenColumns(c).getEnd() //+1
+ );
}
}
af.setMenusFromViewport(af.viewport);
- Desktop.addInternalFrame(af, view.getTitle(),
- view.getWidth(), view.getHeight());
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
+ .getHeight());
//LOAD TREES
///////////////////////////////////////
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());
+ 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()));
+ 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.setTreeFont(new java.awt.Font(view.getFontName(), view
+ .getFontStyle(), tree.getFontSize()));
}
tp.showPlaceholders(tree.getMarkUnlinked());
}
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
////LOAD STRUCTURES
- if(loadTreesAndStructures)
+ if (loadTreesAndStructures)
{
for (int i = 0; i < JSEQ.length; i++)
{
int width = ids[p].getStructureState(s).getWidth();
int height = ids[p].getStructureState(s).getHeight();
- java.awt.Component comp = Desktop.desktop.getComponentAt(x, y);
+ java.awt.Component comp = null;
+
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ for (int f = 0; f < frames.length; f++)
+ {
+ if (frames[f] instanceof AppJmol)
+ {
+ if (frames[f].getX() == x && frames[f].getY() == y
+ && frames[f].getHeight() == height
+ && frames[f].getWidth() == width)
+ {
+ comp = frames[f];
+ break;
+ }
+ }
+ }
+
+ Desktop.desktop.getComponentAt(x, y);
String pdbFile = loadPDBFile(file, ids[p].getId());
jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
- {
- al.getSequenceAt(i)};
+ { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
+ + "") };
- if (comp == null ||
- (comp.getWidth() != width && comp.getHeight() != height))
+ if (comp == null)
{
String state = ids[p].getStructureState(s).getContent();
- StringBuffer newFileLoc = new StringBuffer(state.substring(0,
- state.indexOf("\"", state.indexOf("load")) + 1));
+ 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)));
+ newFileLoc.append(state.substring(state.indexOf("\"", state
+ .indexOf("load \"") + 6)));
- new AppJMol(pdbFile,
- ids[p].getId(),
- seq,
- af.alignPanel,
- newFileLoc.toString(),
- new java.awt.Rectangle(x, y, width, height));
+ new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
+ newFileLoc.toString(), new java.awt.Rectangle(x, y,
+ width, height));
}
- else if(comp!=null)
+ else if (comp != null)
{
StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, null, pdbFile,
+ .setMapping(seq, null, pdbFile,
jalview.io.AppletFormatAdapter.FILE);
- ( (AppJMol) comp).addSequence(seq);
+ ((AppJmol) comp).addSequence(seq);
}
}
}
return af;
}
+ 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);
+ addDatasetRef(vamsasSet.getDatasetId(), ds);
+ }
+ // set the dataset for the newly imported alignment.
+ if (al.getDataset() == null)
+ {
+ al.setDataset(ds);
+ }
+ }
+
+
+ /**
+ *
+ * @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)
+ {
+ jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId());
+ jalview.datamodel.SequenceI dsq = null;
+ if (sq!=null && sq.getDatasetSequence()!=null)
+ {
+ dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
+ }
+
+ String sqid = vamsasSeq.getDsseqid();
+ if (dsq==null)
+ {
+ // need to create or add a new dataset sequence reference to this sequence
+ if (sqid != null)
+ {
+ dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
+ }
+ // 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 = "" + dsq.hashCode();
+ }
+ dsq.setVamsasId(uniqueSetSuffix + sqid);
+ seqRefIds.put(sqid, dsq);
+ if (ds == null)
+ {
+ if (dseqs!=null)
+ {
+ dseqs.addElement(dsq);
+ }
+ }
+ else
+ {
+ ds.addSequence(dsq);
+ }
+ } else {
+ // make this dataset sequence sq's dataset sequence
+ sq.setDatasetSequence(dsq);
+ }
+ }
+ // 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)
+ {
+ StringBuffer sb = new StringBuffer();
+ String newres = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, sq.getSequenceAsString());
+ synchronized (dsq)
+ {
+ sb.append(dsq.getSequence());
+ 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());
+ }
+ System.err
+ .println("DEBUG Notice: Merged dataset sequence ("
+ + (pre ? "prepended" : "") + " "
+ + (post ? "appended" : ""));
+ }
+ }
+
+ java.util.Hashtable datasetIds = null;
+
+ private Alignment getDatasetFor(String datasetId)
+ {
+ if (datasetIds == null)
+ {
+ datasetIds = new Hashtable();
+ return null;
+ }
+ if (datasetIds.containsKey(datasetId))
+ {
+ return (Alignment) datasetIds.get(datasetId);
+ }
+ return null;
+ }
+
+ private void addDatasetRef(String datasetId, Alignment dataset)
+ {
+ if (datasetIds == null)
+ {
+ datasetIds = new Hashtable();
+ }
+ datasetIds.put(datasetId, dataset);
+ }
+
+ private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
+ {
+ for (int d = 0; d < sequence.getDBRefCount(); d++)
+ {
+ 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)
+ {
+ entry.setMap(addMapping(dr.getMapping()));
+ }
+ datasetSequence.addDBRef(entry);
+ }
+ }
+
+ 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)
+ {
+ if (seqRefIds.containsKey(mc.getDseqFor()))
+ {
+ /**
+ * recover from hash
+ */
+ jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor()));
+ }
+ else
+ {
+ frefedSequence.add(new Object[]
+ { mc.getDseqFor(), 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 = ""+ms.hashCode(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen)
+ }
+
+ 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);
+
+ }
+ jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+ addDBRefs(djs, ms);
+
+ }
+ }
+ return (jmap);
+
+ }
+
public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
- boolean keepSeqRefs)
+ boolean keepSeqRefs)
{
- jalview.schemabinding.version2.JalviewModel jm
- = SaveState(ap, null, null, null);
+ jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
+ null, null);
if (!keepSeqRefs)
{