X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=46b75c8860cc67c18c1ad62af9df31abc550bcf4;hb=94ca0419cc7afa75b3c51917a8beaf46a7c05540;hp=ac00b33f60929ab0f3a2551e6f78723b961e60f3;hpb=2ac096ecd8ee1a5c11480e864fce7cf78d661c66;p=jalview.git
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index ac00b33..46b75c8 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,31 +1,29 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
@@ -35,7 +33,9 @@ import jalview.io.vamsas.Datasetsequence;
import jalview.io.vamsas.DatastoreItem;
import jalview.io.vamsas.DatastoreRegistry;
import jalview.io.vamsas.Rangetype;
-import jalview.util.UrlLink;
+import jalview.project.Jalview2XML;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.io.IOException;
import java.util.Enumeration;
@@ -43,23 +43,46 @@ import java.util.HashMap;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
+import java.util.List;
import java.util.Vector;
import java.util.jar.JarInputStream;
import java.util.jar.JarOutputStream;
-import uk.ac.vamsas.client.*;
-import uk.ac.vamsas.objects.core.*;
+import uk.ac.vamsas.client.IClientAppdata;
+import uk.ac.vamsas.client.IClientDocument;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.objects.core.Alignment;
+import uk.ac.vamsas.objects.core.AlignmentSequence;
+import uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation;
+import uk.ac.vamsas.objects.core.AnnotationElement;
+import uk.ac.vamsas.objects.core.DataSet;
+import uk.ac.vamsas.objects.core.DataSetAnnotations;
+import uk.ac.vamsas.objects.core.DbRef;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Glyph;
+import uk.ac.vamsas.objects.core.Local;
+import uk.ac.vamsas.objects.core.MapType;
+import uk.ac.vamsas.objects.core.Mapped;
+import uk.ac.vamsas.objects.core.Property;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.RangeAnnotation;
+import uk.ac.vamsas.objects.core.RangeType;
+import uk.ac.vamsas.objects.core.Seg;
+import uk.ac.vamsas.objects.core.Sequence;
+import uk.ac.vamsas.objects.core.SequenceType;
+import uk.ac.vamsas.objects.core.VAMSAS;
import uk.ac.vamsas.objects.utils.Properties;
/*
- *
+ *
* static {
* org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(
* "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
- *
+ *
*/
/*
- * TODO: check/verify consistency for vamsas sync with group associated alignment annotation
+ * TODO: check/verify consistency for vamsas sync with group associated alignment annotation
*/
public class VamsasAppDatastore
{
@@ -128,7 +151,7 @@ public class VamsasAppDatastore
private void buildSkipList()
{
skipList = new Hashtable();
- AlignFrame[] al = Desktop.getAlignframes();
+ AlignFrame[] al = Desktop.getDesktopAlignFrames();
for (int f = 0; al != null && f < al.length; f++)
{
skipList.put(al[f].getViewport().getSequenceSetId(), al[f]);
@@ -144,11 +167,11 @@ public class VamsasAppDatastore
{
return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
}
- // check if we're working with a string - then workaround
+ // check if we're working with a string - then workaround
// the use of IdentityHashTable because different strings
// have different object IDs.
if (jvobj instanceof String)
- {
+ {
Object seqsetidobj = null;
seqsetidobj = getVamsasObjectBinding().get(jvobj);
if (seqsetidobj != null)
@@ -158,26 +181,27 @@ public class VamsasAppDatastore
// what is expected. object returned by av.getSequenceSetId() -
// reverse lookup to get the 'registered' instance of this string
Vobject obj = getjv2vObj(seqsetidobj);
- if (obj!=null && !(obj instanceof Alignment))
+ if (obj != null && !(obj instanceof Alignment))
{
- Cache.log.warn("IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
- + seqsetidobj + " to object " + obj);
+ Console.warn(
+ "IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
+ + seqsetidobj + " to object " + obj);
}
return obj;
}
else
{
- Cache.log.warn("Unexpected mapping for Jalview String Object ID "
- + seqsetidobj
- + " to another jalview dataset object " + seqsetidobj);
+ Console.warn("Unexpected mapping for Jalview String Object ID "
+ + seqsetidobj + " to another jalview dataset object "
+ + seqsetidobj);
}
}
}
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Returning null VorbaID binding for jalview object "
- + jvobj);
+ Console.debug(
+ "Returning null VorbaID binding for jalview object " + jvobj);
}
return null;
}
@@ -193,8 +217,8 @@ public class VamsasAppDatastore
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log
- .debug("Registering new object and returning null for getvObj2jv");
+ Console.debug(
+ "Registering new object and returning null for getvObj2jv");
return null;
}
if (vobj2jv.containsKey(vobj.getVorbaId()))
@@ -213,36 +237,38 @@ public class VamsasAppDatastore
if (id == null || vobj.getVorbaId() == null
|| cdoc.getObject(id) != vobj)
{
- Cache.log.error("Failed to get id for "
+ Console.error("Failed to get id for "
+ (vobj.isRegisterable() ? "registerable"
- : "unregisterable") + " object " + vobj);
+ : "unregisterable")
+ + " object " + vobj);
}
}
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing vamsas id binding for "
- + vobj.getVorbaId(), new Exception(
- "Overwriting vamsas id binding."));
+ + vobj.getVorbaId(),
+ new Exception(MessageManager.getString(
+ "exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing jalview object binding for "
- + jvobj, new Exception(
- "Overwriting jalview object binding."));
+ + jvobj,
+ new Exception("Overwriting jalview object binding."));
}
/*
- * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
+ * Cache.error("Attempt to make conflicting object binding! "+vobj+" id "
* +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
* already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
* bindjvvobj")); }
*/
// we just update the hash's regardless!
- Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
+ Console.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
@@ -252,10 +278,11 @@ public class VamsasAppDatastore
* put the alignment viewed by AlignViewport into cdoc.
*
* @param av
- * alignViewport to be stored
+ * alignViewport to be stored
* @param aFtitle
- * title for alignment
- * @return true if alignment associated with viewport was stored/synchronized to document
+ * title for alignment
+ * @return true if alignment associated with viewport was stored/synchronized
+ * to document
*/
public boolean storeVAMSAS(AlignViewport av, String aFtitle)
{
@@ -270,26 +297,29 @@ public class VamsasAppDatastore
DataSet dataset = null;
if (jds == null)
{
- Cache.log.warn("Creating new dataset for an alignment.");
+ Console.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
jds = jal.getDataset();
}
-
+
// try and get alignment and association for sequence set id
Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId());
- if (alignment!=null)
+ if (alignment != null)
{
dataset = (DataSet) alignment.getV_parent();
- } else {
- // is the dataset already registered
- dataset = (DataSet) getjv2vObj(jds);
}
-
+ else
+ {
+ // is the dataset already registered
+ dataset = (DataSet) getjv2vObj(jds);
+ }
+
if (dataset == null)
{
// it might be that one of the dataset sequences does actually have a
- // binding, so search for it indirectly. If it does, then the local jalview dataset
+ // binding, so search for it indirectly. If it does, then the local
+ // jalview dataset
// must be merged with the existing vamsas dataset.
jalview.datamodel.SequenceI[] jdatset = jds.getSequencesArray();
for (int i = 0; i < jdatset.length; i++)
@@ -305,12 +335,11 @@ public class VamsasAppDatastore
}
else
{
- if (vbound.getV_parent()!=null && dataset != vbound.getV_parent())
+ if (vbound.getV_parent() != null
+ && dataset != vbound.getV_parent())
{
throw new Error(
"IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.");
- // This occurs because the dataset for the alignment we are
- // trying to
}
}
}
@@ -320,7 +349,7 @@ public class VamsasAppDatastore
if (dataset == null)
{
- Cache.log.warn("Creating new vamsas dataset for alignment view "
+ Console.warn("Creating new vamsas dataset for alignment view "
+ av.getSequenceSetId());
// we create a new dataset on the default vamsas root.
root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
@@ -341,7 +370,8 @@ public class VamsasAppDatastore
// flag.
// this *will* break when alignment contains both nucleotide and amino
// acid sequences.
- String dict = jal.isNucleotide() ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+ String dict = jal.isNucleotide()
+ ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
: uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
Vector dssmods = new Vector();
for (int i = 0; i < jal.getHeight(); i++)
@@ -350,11 +380,14 @@ public class VamsasAppDatastore
// referenced
// sequences
// to dataset.
- Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(this, sq, dict, dataset);
+ Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(this,
+ sq, dict, dataset);
sequence = (Sequence) dssync.getVobj();
- if (dssync.getModified()) {
- dssmods.addElement(sequence);
- };
+ if (dssync.getModified())
+ {
+ dssmods.addElement(sequence);
+ }
+ ;
}
if (dssmods.size() > 0)
{
@@ -406,8 +439,8 @@ public class VamsasAppDatastore
else
{
// always prepare to clone the alignment
- boolean alismod = av.isUndoRedoHashModified((long[]) alignRDHash
- .get(av.getSequenceSetId()));
+ boolean alismod = av.isUndoRedoHashModified(
+ (long[]) alignRDHash.get(av.getSequenceSetId()));
// todo: verify and update mutable alignment props.
// TODO: Use isLocked methods
if (alignment.getModifiable() == null
@@ -416,8 +449,8 @@ public class VamsasAppDatastore
{
boolean modified = false;
// check existing sequences in local and in document.
- Vector docseqs = new Vector(alignment
- .getAlignmentSequenceAsReference());
+ Vector docseqs = new Vector(
+ alignment.getAlignmentSequenceAsReference());
for (int i = 0; i < jal.getHeight(); i++)
{
modified |= syncToAlignmentSequence(jal.getSequenceAt(i),
@@ -427,8 +460,8 @@ public class VamsasAppDatastore
{
// removeValignmentSequences(alignment, docseqs);
docseqs.removeAllElements();
- System.out
- .println("Sequence deletion from alignment is not implemented.");
+ jalview.bin.Console.outPrintln(
+ "Sequence deletion from alignment is not implemented.");
}
if (modified)
@@ -455,11 +488,11 @@ public class VamsasAppDatastore
}
if (alismod)
{
- System.out.println("update alignment in document.");
+ jalview.bin.Console.outPrintln("update alignment in document.");
}
else
{
- System.out.println("alignment in document left unchanged.");
+ jalview.bin.Console.outPrintln("alignment in document left unchanged.");
}
}
else
@@ -467,17 +500,18 @@ public class VamsasAppDatastore
// unbind alignment from view.
// create new binding and new alignment.
// mark trail on new alignment as being derived from old ?
- System.out
- .println("update edited alignment to new alignment in document.");
+ jalview.bin.Console.outPrintln(
+ "update edited alignment to new alignment in document.");
}
}
// ////////////////////////////////////////////
// SAVE Alignment Sequence Features
- for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
+ for (int i = 0, iSize = alignment
+ .getAlignmentSequenceCount(); i < iSize; i++)
{
AlignmentSequence valseq;
- SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment
- .getAlignmentSequence(i));
+ SequenceI alseq = (SequenceI) getvObj2jv(
+ valseq = alignment.getAlignmentSequence(i));
if (alseq != null && alseq.getSequenceFeatures() != null)
{
/*
@@ -488,16 +522,17 @@ public class VamsasAppDatastore
* jalview.datamodel.SequenceFeature[] features = alseq
* .getSequenceFeatures(); for (int f = 0; f < features.length; f++) {
* if (features[f] != null) { AlignmentSequenceAnnotation valseqf = (
- * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf ==
- * null) {
+ * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf
+ * == null) {
*
* valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
* new AlignmentSequenceAnnotation(), features[i]);
* valseqf.setGraph(false);
- * valseqf.addProperty(newProperty("jalview:feature","boolean","true"));
- * if (valseqf.getProvenance() == null) { valseqf.setProvenance(new
- * Provenance()); } addProvenance(valseqf.getProvenance(), "created"); //
- * JBPNote - // need to // update bindjvvobj(features[i], valseqf);
+ * valseqf.addProperty(newProperty("jalview:feature"
+ * ,"boolean","true")); if (valseqf.getProvenance() == null) {
+ * valseqf.setProvenance(new Provenance()); }
+ * addProvenance(valseqf.getProvenance(), "created"); // JBPNote - //
+ * need to // update bindjvvobj(features[i], valseqf);
* valseq.addAlignmentSequenceAnnotation(valseqf); } } }
*/
}
@@ -518,10 +553,11 @@ public class VamsasAppDatastore
{
continue;
}
- if (aa[i].groupRef!=null)
+ if (aa[i].groupRef != null)
{
// TODO: store any group associated annotation references
- Cache.log.warn("Group associated sequence annotation is not stored in VAMSAS document.");
+ Console.warn(
+ "Group associated sequence annotation is not stored in VAMSAS document.");
continue;
}
if (aa[i].sequenceRef != null)
@@ -536,12 +572,8 @@ public class VamsasAppDatastore
else
{
// first find the alignment sequence to associate this with.
- SequenceI jvalsq = null;
- Enumeration jval = av.getAlignment().getSequences()
- .elements();
- while (jval.hasMoreElements())
+ for (SequenceI jvalsq : av.getAlignment().getSequences())
{
- jvalsq = (SequenceI) jval.nextElement();
// saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence)
// sref, aa[i]);
if (jvalsq.getDatasetSequence() == aa[i].sequenceRef)
@@ -558,7 +590,8 @@ public class VamsasAppDatastore
else
{
// add Alignment Annotation
- uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
+ uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(
+ aa[i]);
if (an == null)
{
an = new uk.ac.vamsas.objects.core.AlignmentAnnotation();
@@ -607,8 +640,8 @@ public class VamsasAppDatastore
ae = new AnnotationElement();
ae.setDescription(aa[i].annotations[a].description);
ae.addGlyph(new Glyph());
- ae.getGlyph(0).setContent(
- aa[i].annotations[a].displayCharacter); // assume
+ ae.getGlyph(0)
+ .setContent(aa[i].annotations[a].displayCharacter); // assume
// jax-b
// takes
// care
@@ -623,11 +656,10 @@ public class VamsasAppDatastore
if (aa[i].annotations[a].secondaryStructure != ' ')
{
Glyph ss = new Glyph();
- ss
- .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
- ss
- .setContent(String
- .valueOf(aa[i].annotations[a].secondaryStructure));
+ ss.setDict(
+ uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+ ss.setContent(String.valueOf(
+ aa[i].annotations[a].secondaryStructure));
ae.addGlyph(ss);
}
an.addAnnotationElement(ae);
@@ -647,12 +679,14 @@ public class VamsasAppDatastore
an.setGroup(Integer.toString(aa[i].graphGroup));
if (aa[i].threshold != null && aa[i].threshold.displayed)
{
- an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE, ""
- + aa[i].threshold.value));
+ an.addProperty(Properties.newProperty(THRESHOLD,
+ Properties.FLOATTYPE,
+ "" + aa[i].threshold.value));
if (aa[i].threshold.label != null)
{
- an.addProperty(Properties.newProperty(THRESHOLD + "Name", Properties.STRINGTYPE,
- "" + aa[i].threshold.label));
+ an.addProperty(Properties.newProperty(
+ THRESHOLD + "Name", Properties.STRINGTYPE,
+ "" + aa[i].threshold.label));
}
}
}
@@ -665,14 +699,14 @@ public class VamsasAppDatastore
// LOCK METHODS)
{
// verify annotation - update (perhaps)
- Cache.log
- .info("update alignment sequence annotation. not yet implemented.");
+ Console.info(
+ "update alignment sequence annotation. not yet implemented.");
}
else
{
// verify annotation - update (perhaps)
- Cache.log
- .info("updated alignment sequence annotation added.");
+ Console.info(
+ "updated alignment sequence annotation added.");
}
}
}
@@ -695,7 +729,8 @@ public class VamsasAppDatastore
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.getViewPort().getSequenceSetId().equals(av.getSequenceSetId()))
+ if (tp.getViewPort().getSequenceSetId()
+ .equals(av.getSequenceSetId()))
{
DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
jal, alignment);
@@ -716,17 +751,20 @@ public class VamsasAppDatastore
}
/**
- * very quick test to see if the viewport would be stored in the vamsas document.
- * Reasons for not storing include the unaligned flag being false (for all sequences, including the hidden ones!)
+ * very quick test to see if the viewport would be stored in the vamsas
+ * document. Reasons for not storing include the unaligned flag being false
+ * (for all sequences, including the hidden ones!)
+ *
* @param av
- * @return true if alignment associated with this view will be stored in document.
+ * @return true if alignment associated with this view will be stored in
+ * document.
*/
- public boolean alignmentWillBeSkipped(AlignViewport av)
+ public boolean alignmentWillBeSkipped(AlignmentViewport av)
{
return (!av.getAlignment().isAligned());
}
- private void addToSkipList(AlignViewport av)
+ private void addToSkipList(AlignmentViewport av)
{
if (skipList == null)
{
@@ -742,18 +780,19 @@ public class VamsasAppDatastore
* @param alignment
* @param docseqs
*/
- private void removeValignmentSequences(Alignment alignment, Vector docseqs)
+ private void removeValignmentSequences(Alignment alignment,
+ Vector docseqs)
{
// delete these from document. This really needs to be a generic document
// API function derived by CASTOR.
Enumeration en = docseqs.elements();
while (en.hasMoreElements())
{
- alignment.removeAlignmentSequence((AlignmentSequence) en
- .nextElement());
+ alignment.removeAlignmentSequence(
+ (AlignmentSequence) en.nextElement());
}
- Entry pe = addProvenance(alignment.getProvenance(), "Removed "
- + docseqs.size() + " sequences");
+ Entry pe = addProvenance(alignment.getProvenance(),
+ "Removed " + docseqs.size() + " sequences");
en = alignment.enumerateAlignmentAnnotation();
Vector toremove = new Vector();
while (en.hasMoreElements())
@@ -792,8 +831,8 @@ public class VamsasAppDatastore
en = toremove.elements();
while (en.hasMoreElements())
{
- alignment
- .removeAlignmentAnnotation((uk.ac.vamsas.objects.core.AlignmentAnnotation) en
+ alignment.removeAlignmentAnnotation(
+ (uk.ac.vamsas.objects.core.AlignmentAnnotation) en
.nextElement());
}
// TODO: search through alignment annotations to remove any references to
@@ -842,17 +881,16 @@ public class VamsasAppDatastore
modal = true;
alseq.setName(jvalsq.getName());
}
- if (jvalsq.getDescription() != null
- && (alseq.getDescription() == null || !jvalsq.getDescription()
- .equals(alseq.getDescription())))
+ if (jvalsq.getDescription() != null && (alseq.getDescription() == null
+ || !jvalsq.getDescription().equals(alseq.getDescription())))
{
modal = true;
alseq.setDescription(jvalsq.getDescription());
}
if (getjv2vObj(jvalsq.getDatasetSequence()) == null)
{
- Cache.log
- .warn("Serious Implementation error - Unbound dataset sequence in alignment: "
+ Console.warn(
+ "Serious Implementation error - Unbound dataset sequence in alignment: "
+ jvalsq.getDatasetSequence());
}
alseq.setRefid(getjv2vObj(jvalsq.getDatasetSequence()));
@@ -871,7 +909,7 @@ public class VamsasAppDatastore
* creates/syncs the jvalsq from the alignment sequence
*/
private boolean syncFromAlignmentSequence(AlignmentSequence valseq,
- char valGapchar, char gapChar, Vector dsseqs)
+ char valGapchar, char gapChar, List dsseqs)
{
boolean modal = false;
@@ -892,8 +930,8 @@ public class VamsasAppDatastore
|| !valseq.getSequence().equals(alseq.getSequenceAsString()))
{
// this might go *horribly* wrong
- alseq.setSequence(new String(valseq.getSequence()).replace(
- valGapchar, gapChar));
+ alseq.setSequence(new String(valseq.getSequence())
+ .replace(valGapchar, gapChar));
alseq.setStart((int) valseq.getStart());
alseq.setEnd((int) valseq.getEnd());
modal = true;
@@ -903,36 +941,39 @@ public class VamsasAppDatastore
modal = true;
alseq.setName(valseq.getName());
}
- if (alseq.getDescription()==null || (valseq.getDescription() != null && !alseq.getDescription()
- .equals(valseq.getDescription())))
+ if (alseq.getDescription() == null || (valseq.getDescription() != null
+ && !alseq.getDescription().equals(valseq.getDescription())))
{
alseq.setDescription(valseq.getDescription());
modal = true;
}
- if (modal && Cache.log.isDebugEnabled())
+ if (modal && Console.isDebugEnabled())
{
- Cache.log.debug("Updating apparently edited sequence "
- + alseq.getName());
+ Console.debug(
+ "Updating apparently edited sequence " + alseq.getName());
}
}
else
{
- alseq = new jalview.datamodel.Sequence(valseq.getName(), valseq
- .getSequence().replace(valGapchar, gapChar), (int) valseq
- .getStart(), (int) valseq.getEnd());
-
+ alseq = new jalview.datamodel.Sequence(valseq.getName(),
+ valseq.getSequence().replace(valGapchar, gapChar),
+ (int) valseq.getStart(), (int) valseq.getEnd());
+
Vobject datsetseq = (Vobject) valseq.getRefid();
if (datsetseq != null)
{
alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
- if (valseq.getDescription()!=null)
+ if (valseq.getDescription() != null)
{
alseq.setDescription(valseq.getDescription());
- } else {
+ }
+ else
+ {
// inherit description line from dataset.
- if (alseq.getDatasetSequence().getDescription()!=null)
+ if (alseq.getDatasetSequence().getDescription() != null)
{
- alseq.setDescription(alseq.getDatasetSequence().getDescription());
+ alseq.setDescription(
+ alseq.getDatasetSequence().getDescription());
}
}
// if
@@ -945,8 +986,8 @@ public class VamsasAppDatastore
}
else
{
- Cache.log
- .error("Invalid dataset sequence id (null) for alignment sequence "
+ Console.error(
+ "Invalid dataset sequence id (null) for alignment sequence "
+ valseq.getVorbaId());
}
bindjvvobj(alseq, valseq);
@@ -1016,10 +1057,10 @@ public class VamsasAppDatastore
{
// we only write an annotation where it really exists.
Glyph ss = new Glyph();
- ss
- .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
- ss.setContent(String
- .valueOf(alan.annotations[a].secondaryStructure));
+ ss.setDict(
+ uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+ ss.setContent(
+ String.valueOf(alan.annotations[a].secondaryStructure));
ae.addGlyph(ss);
}
an.addAnnotationElement(ae);
@@ -1034,7 +1075,8 @@ public class VamsasAppDatastore
// uk.ac.vamsas.
// objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
// objects.core.AlignmentSequence) sref;
- uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(alan);
+ uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(
+ alan);
int[] gapMap = getGapMap(AlSeqMaps, alan);
if (an == null)
{
@@ -1055,12 +1097,13 @@ public class VamsasAppDatastore
// bits.
if (alan.getThreshold() != null && alan.getThreshold().displayed)
{
- an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE,
- ""
- + alan.getThreshold().value));
+ an.addProperty(Properties.newProperty(THRESHOLD,
+ Properties.FLOATTYPE, "" + alan.getThreshold().value));
if (alan.getThreshold().label != null)
- an.addProperty(Properties.newProperty(THRESHOLD + "Name", Properties.STRINGTYPE, ""
- + alan.getThreshold().label));
+ {
+ an.addProperty(Properties.newProperty(THRESHOLD + "Name",
+ Properties.STRINGTYPE, "" + alan.getThreshold().label));
+ }
}
((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
bindjvvobj(alan, an);
@@ -1072,13 +1115,13 @@ public class VamsasAppDatastore
// METHODS)
{
// verify existing alignment sequence annotation is up to date
- System.out.println("update dataset sequence annotation.");
+ jalview.bin.Console.outPrintln("update dataset sequence annotation.");
}
else
{
// verify existing alignment sequence annotation is up to date
- System.out
- .println("make new alignment dataset sequence annotation if modification has happened.");
+ jalview.bin.Console.outPrintln(
+ "make new alignment dataset sequence annotation if modification has happened.");
}
}
@@ -1111,7 +1154,8 @@ public class VamsasAppDatastore
// uk.ac.vamsas.
// objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
// objects.core.AlignmentSequence) sref;
- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(alan);
+ uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(
+ alan);
int[] gapMap = getGapMap(AlSeqMaps, alan);
if (an == null)
{
@@ -1140,13 +1184,13 @@ public class VamsasAppDatastore
// METHODS)
{
// verify existing alignment sequence annotation is up to date
- System.out.println("update alignment sequence annotation.");
+ jalview.bin.Console.outPrintln("update alignment sequence annotation.");
}
else
{
// verify existing alignment sequence annotation is up to date
- System.out
- .println("make new alignment sequence annotation if modification has happened.");
+ jalview.bin.Console.outPrintln(
+ "make new alignment sequence annotation if modification has happened.");
}
}
}
@@ -1186,24 +1230,25 @@ public class VamsasAppDatastore
switch (alan.graph)
{
case AlignmentAnnotation.BAR_GRAPH:
- an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION, Properties.BOOLEANTYPE, "true"));
+ an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION,
+ Properties.BOOLEANTYPE, "true"));
break;
case AlignmentAnnotation.LINE_GRAPH:
- an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION, Properties.BOOLEANTYPE, "true"));
+ an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION,
+ Properties.BOOLEANTYPE, "true"));
break;
default:
// don't add any kind of discrete or continous property info.
}
}
-
/**
* get start 1)
{
@@ -1389,7 +1437,8 @@ public class VamsasAppDatastore
// to the align frames.
boolean gathered = false;
String newviewid = null;
- AlignedCodonFrame[] mappings = av.getAlignment().getCodonFrames();
+ List mappings = av.getAlignment()
+ .getCodonFrames();
for (int i = 0; i < views.length; i++)
{
if (views[i] != av)
@@ -1424,18 +1473,19 @@ public class VamsasAppDatastore
{
// ensure sequence mappings from vamsas document view still
// active
- if (mappings != null && mappings.length > 0)
+ if (mappings != null)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().addMappings(mappings);
+ .getStructureSelectionManager(Desktop.instance)
+ .registerMappings(mappings);
}
}
}
// ensure vamsas object binds to the stored views retrieved from
// Jalview appdata
- //jalview.structure.StructureSelectionManager
- // .getStructureSelectionManager()
- // .addStructureViewerListener(viewframe.alignPanel);
+ // jalview.structure.StructureSelectionManager
+ // .getStructureSelectionManager()
+ // .addStructureViewerListener(viewframe.alignPanel);
}
@@ -1448,18 +1498,22 @@ public class VamsasAppDatastore
* binding tables
*
* @param oldjvobject
- * @param newjvobject (may be null)
+ * @param newjvobject
+ * (may be null)
*/
private void replaceJvObjMapping(Object oldjvobject, Object newjvobject)
{
Object vobject = jv2vobj.remove(oldjvobject);
if (vobject == null)
{
- throw new Error(
- "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
- + oldjvobject + ")");
+ // NOTE: this happens if user deletes object in one session then updates
+ // from another client
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_old_jalview_object_not_bound",
+ new String[]
+ { oldjvobject.toString() }));
}
- if (newjvobject!=null)
+ if (newjvobject != null)
{
jv2vobj.put(newjvobject, vobject);
vobj2jv.put(vobject, newjvobject);
@@ -1476,29 +1530,28 @@ public class VamsasAppDatastore
{
try
{
- jalview.gui.Jalview2XML jxml = new jalview.gui.Jalview2XML();
+ Jalview2XML jxml = new Jalview2XML();
jxml.setObjectMappingTables(mapKeysToString(vobj2jv),
mapValuesToString(jv2vobj));
jxml.setSkipList(skipList);
if (dojvsync)
{
- jxml.SaveState(new JarOutputStream(cappdata
- .getClientOutputStream()));
+ jxml.saveState(
+ new JarOutputStream(cappdata.getClientOutputStream()));
}
} catch (Exception e)
{
// TODO raise GUI warning if user requests it.
- jalview.bin.Cache.log
- .error(
- "Couldn't update jalview client application data. Giving up - local settings probably lost.",
- e);
+ Console.error(
+ "Couldn't update jalview client application data. Giving up - local settings probably lost.",
+ e);
}
}
else
{
- jalview.bin.Cache.log
- .error("Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
+ Console.error(
+ "Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
}
}
@@ -1537,8 +1590,10 @@ public class VamsasAppDatastore
}
return mapped;
}
+
/**
* synchronize Jalview from the vamsas document
+ *
* @return number of new views from document
*/
public int updateToJalview()
@@ -1555,18 +1610,19 @@ public class VamsasAppDatastore
// ///LOAD DATASET
DataSet dataset = root.getDataSet(_ds);
int i, iSize = dataset.getSequenceCount();
- Vector dsseqs;
- jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
+ List dsseqs;
+ jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(
+ dataset);
int jremain = 0;
if (jdataset == null)
{
- Cache.log.debug("Initialising new jalview dataset fields");
+ Console.debug("Initialising new jalview dataset fields");
newds = true;
dsseqs = new Vector();
}
else
{
- Cache.log.debug("Update jalview dataset from vamsas.");
+ Console.debug("Update jalview dataset from vamsas.");
jremain = jdataset.getHeight();
dsseqs = jdataset.getSequences();
}
@@ -1574,12 +1630,12 @@ public class VamsasAppDatastore
// TODO: test sequence merging - we preserve existing non vamsas
// sequences but add in any new vamsas ones, and don't yet update any
// sequence attributes
- for (i = 0; i < iSize
- ; i++)
+ for (i = 0; i < iSize; i++)
{
Sequence vdseq = dataset.getSequence(i);
- jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence(this, vdseq);
-
+ jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence(
+ this, vdseq);
+
jalview.datamodel.SequenceI dsseq = (SequenceI) dssync.getJvobj();
if (dssync.isAddfromdoc())
{
@@ -1602,40 +1658,43 @@ public class VamsasAppDatastore
SequenceI[] seqs = new SequenceI[dsseqs.size()];
for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
{
- seqs[i] = (SequenceI) dsseqs.elementAt(i);
- dsseqs.setElementAt(null, i);
+ seqs[i] = dsseqs.get(i);
+ dsseqs.set(i, null);
}
jdataset = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas dataset imported into jalview.");
+ Console.debug("New vamsas dataset imported into jalview.");
bindjvvobj(jdataset, dataset);
}
// ////////
// add any new dataset sequence feature annotations
if (dataset.getDataSetAnnotations() != null)
{
- for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)
+ for (int dsa = 0; dsa < dataset
+ .getDataSetAnnotationsCount(); dsa++)
{
DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa);
// TODO: deal with group annotation on datset sequences.
if (dseta.getSeqRefCount() == 1)
{
- SequenceI dsSeq = (SequenceI) getvObj2jv((Vobject) dseta
- .getSeqRef(0)); // TODO: deal with group dataset
+ SequenceI dsSeq = (SequenceI) getvObj2jv(
+ (Vobject) dseta.getSeqRef(0)); // TODO: deal with group
+ // dataset
// annotations
if (dsSeq == null)
{
- jalview.bin.Cache.log
- .warn("Couldn't resolve jalview sequenceI for dataset object reference "
- + ((Vobject) dataset.getDataSetAnnotations(
- dsa).getSeqRef(0)).getVorbaId()
- .getId());
+ Console.warn(
+ "Couldn't resolve jalview sequenceI for dataset object reference "
+ + ((Vobject) dataset
+ .getDataSetAnnotations(dsa)
+ .getSeqRef(0)).getVorbaId()
+ .getId());
}
else
{
if (dseta.getAnnotationElementCount() == 0)
{
new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq);
-
+
}
else
{
@@ -1644,12 +1703,15 @@ public class VamsasAppDatastore
// JBPNote: we could just add them to all alignments but
// that may complicate cross references in the jalview
// datamodel
- Cache.log
- .warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
+ Console.warn(
+ "Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
}
}
- } else {
- Cache.log.warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
+ }
+ else
+ {
+ Console.warn(
+ "Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
}
}
}
@@ -1657,12 +1719,13 @@ public class VamsasAppDatastore
{
// LOAD ALIGNMENTS from DATASET
- for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++)
+ for (int al = 0, nal = dataset
+ .getAlignmentCount(); al < nal; al++)
{
uk.ac.vamsas.objects.core.Alignment alignment = dataset
.getAlignment(al);
// TODO check this handles multiple views properly
- AlignViewport av = findViewport(alignment);
+ AlignmentViewport av = findViewport(alignment);
jalview.datamodel.AlignmentI jal = null;
if (av != null)
@@ -1670,9 +1733,9 @@ public class VamsasAppDatastore
// TODO check that correct alignment object is retrieved when
// hidden seqs exist.
jal = (av.hasHiddenRows()) ? av.getAlignment()
- .getHiddenSequences().getFullAlignment() : av
- .getAlignment();
- }
+ .getHiddenSequences().getFullAlignment()
+ : av.getAlignment();
+ }
iSize = alignment.getAlignmentSequenceCount();
boolean refreshal = false;
Vector newasAnnots = new Vector();
@@ -1691,10 +1754,10 @@ public class VamsasAppDatastore
for (i = 0; i < iSize; i++)
{
AlignmentSequence valseq = alignment.getAlignmentSequence(i);
- jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq);
+ jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(
+ valseq);
if (syncFromAlignmentSequence(valseq, valGapchar, gapChar,
- dsseqs)
- && alseq != null)
+ dsseqs) && alseq != null)
{
// updated to sequence from the document
@@ -1707,7 +1770,8 @@ public class VamsasAppDatastore
.getAlignmentSequenceAnnotation();
for (int a = 0; a < vasannot.length; a++)
{
- jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO:
+ jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(
+ vasannot[a]); // TODO:
// 1:many
// jalview
// alignment
@@ -1742,8 +1806,8 @@ public class VamsasAppDatastore
// OBJECT LOCK
// METHODS)
{
- Cache.log
- .info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
+ Console.info(
+ "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
// TODO: should at least replace with new one - otherwise
// things will break
// basically do this:
@@ -1762,21 +1826,22 @@ public class VamsasAppDatastore
SequenceI[] seqs = new SequenceI[dsseqs.size()];
for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
{
- seqs[i] = (SequenceI) dsseqs.elementAt(i);
- dsseqs.setElementAt(null, i);
+ seqs[i] = dsseqs.get(i);
+ dsseqs.set(i, null);
}
jal = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas alignment imported into jalview "
+ Console.debug("New vamsas alignment imported into jalview "
+ alignment.getVorbaId().getId());
jal.setDataset(jdataset);
}
if (newasAnnots != null && newasAnnots.size() > 0)
{
// Add the new sequence annotations in to the alignment.
- for (int an = 0, anSize = newasAnnots.size(); an < anSize; an++)
+ for (int an = 0, anSize = newasAnnots
+ .size(); an < anSize; an++)
{
- jal.addAnnotation((AlignmentAnnotation) newasAnnots
- .elementAt(an));
+ jal.addAnnotation(
+ (AlignmentAnnotation) newasAnnots.elementAt(an));
// TODO: check if anything has to be done - like calling
// adjustForAlignment or something.
newasAnnots.setElementAt(null, an);
@@ -1793,7 +1858,8 @@ public class VamsasAppDatastore
for (int j = 0; j < an.length; j++)
{
- jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);
+ jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(
+ an[j]);
if (jan != null)
{
// update or stay the same.
@@ -1803,16 +1869,16 @@ public class VamsasAppDatastore
// jan.update(getjAlignmentAnnotation(jal, an[a])); // update
// from another annotation object in place.
- Cache.log
- .debug("update from vamsas alignment annotation to existing jalview alignment annotation.");
+ Console.debug(
+ "update from vamsas alignment annotation to existing jalview alignment annotation.");
if (an[j].getModifiable() == null) // TODO: USE VAMSAS
// LIBRARY OBJECT LOCK
// METHODS)
{
// TODO: user defined annotation is totally mutable... - so
// load it up or throw away if locally edited.
- Cache.log
- .info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
+ Console.info(
+ "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
}
// TODO: compare annotation element rows
// TODO: compare props.
@@ -1820,7 +1886,8 @@ public class VamsasAppDatastore
else
{
jan = getjAlignmentAnnotation(jal, an[j]);
- // TODO: ensure we add the alignment annotation before the automatic annotation rows
+ // TODO: ensure we add the alignment annotation before the
+ // automatic annotation rows
jal.addAnnotation(jan);
bindjvvobj(jan, an[j]);
refreshal = true;
@@ -1830,21 +1897,23 @@ public class VamsasAppDatastore
AlignFrame alignFrame;
if (av == null)
{
- Cache.log.debug("New alignframe for alignment "
+ Console.debug("New alignframe for alignment "
+ alignment.getVorbaId());
// ///////////////////////////////
// construct alignment view
alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT, alignment.getVorbaId()
- .toString());
+ AlignFrame.DEFAULT_HEIGHT,
+ alignment.getVorbaId().toString());
av = alignFrame.getViewport();
newAlignmentViews.addElement(av);
- String title = alignment.getProvenance().getEntry(
- alignment.getProvenance().getEntryCount() - 1)
+ String title = alignment.getProvenance()
+ .getEntry(
+ alignment.getProvenance().getEntryCount() - 1)
.getAction();
if (alignment.getPropertyCount() > 0)
{
- for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++)
+ for (int p = 0, pe = alignment
+ .getPropertyCount(); p < pe; p++)
{
if (alignment.getProperty(p).getName().equals("title"))
{
@@ -1854,7 +1923,7 @@ public class VamsasAppDatastore
}
// TODO: automatically create meaningful title for a vamsas
// alignment using its provenance.
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
title = title + "(" + alignment.getVorbaId() + ")";
@@ -1888,7 +1957,7 @@ public class VamsasAppDatastore
TreePanel tp = null;
if (vstree.isValidTree())
{
- tp = alignFrame.ShowNewickTree(vstree.getNewickTree(),
+ tp = alignFrame.showNewickTree(vstree.getNewickTree(),
vstree.getTitle(), vstree.getInputData(), 600,
500, t * 20 + 50, t * 20 + 50);
@@ -1901,12 +1970,12 @@ public class VamsasAppDatastore
vstree.UpdateSequenceTreeMap(tp);
} catch (RuntimeException e)
{
- Cache.log.warn("update of labels failed.", e);
+ Console.warn("update of labels failed.", e);
}
}
else
{
- Cache.log.warn("Cannot create tree for tree " + t
+ Console.warn("Cannot create tree for tree " + t
+ " in document ("
+ alignment.getTree(t).getVorbaId());
}
@@ -1923,7 +1992,8 @@ public class VamsasAppDatastore
DataSet dataset = root.getDataSet(_ds);
if (dataset.getSequenceMappingCount() > 0)
{
- for (int sm = 0, smCount = dataset.getSequenceMappingCount(); sm < smCount; sm++)
+ for (int sm = 0, smCount = dataset
+ .getSequenceMappingCount(); sm < smCount; sm++)
{
Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this,
dataset.getSequenceMapping(sm));
@@ -1934,10 +2004,10 @@ public class VamsasAppDatastore
return newAlignmentViews.size();
}
- public AlignViewport findViewport(Alignment alignment)
+ public AlignmentViewport findViewport(Alignment alignment)
{
- AlignViewport av = null;
- AlignViewport[] avs = Desktop
+ AlignmentViewport av = null;
+ AlignmentViewport[] avs = Desktop
.getViewports((String) getvObj2jv(alignment));
if (avs != null)
{
@@ -1980,11 +2050,11 @@ public class VamsasAppDatastore
// may not quite cope with this (without binding an array of annotations to
// a vamsas alignment annotation)
// summary flags saying what we found over the set of annotation rows.
- boolean[] AeContent = new boolean[]
- { false, false, false, false, false };
+ boolean[] AeContent = new boolean[] { false, false, false, false,
+ false };
int[] rangeMap = getMapping(annotation);
- jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
- { new jalview.datamodel.Annotation[rangeMap.length],
+ jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][] {
+ new jalview.datamodel.Annotation[rangeMap.length],
new jalview.datamodel.Annotation[rangeMap.length] };
boolean mergeable = true; // false if 'after positions cant be placed on
// same annotation row as positions.
@@ -2002,7 +2072,7 @@ public class VamsasAppDatastore
if (anot[row][pos] != null)
{
// only time this should happen is if the After flag is set.
- Cache.log.debug("Ignoring duplicate annotation site at " + pos);
+ Console.debug("Ignoring duplicate annotation site at " + pos);
continue;
}
if (anot[1 - row][pos] != null)
@@ -2029,20 +2099,16 @@ public class VamsasAppDatastore
Glyph[] glyphs = ae[aa].getGlyph();
for (int g = 0; g < glyphs.length; g++)
{
- if (glyphs[g]
- .getDict()
- .equals(
- uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
+ if (glyphs[g].getDict().equals(
+ uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
{
ss = glyphs[g].getContent();
AeContent[HASSECSTR] = true;
}
- else if (glyphs[g]
- .getDict()
- .equals(
- uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
+ else if (glyphs[g].getDict().equals(
+ uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
{
- Cache.log.debug("ignoring hydrophobicity glyph marker.");
+ Console.debug("ignoring hydrophobicity glyph marker.");
AeContent[HASHPHOB] = true;
char c = (dc = glyphs[g].getContent()).charAt(0);
// dc may get overwritten - but we still set the colour.
@@ -2058,8 +2124,8 @@ public class VamsasAppDatastore
}
else
{
- Cache.log
- .debug("IMPLEMENTATION TODO: Ignoring unknown glyph type "
+ Console.debug(
+ "IMPLEMENTATION TODO: Ignoring unknown glyph type "
+ glyphs[g].getDict());
}
}
@@ -2070,28 +2136,28 @@ public class VamsasAppDatastore
AeContent[HASVALS] = true;
if (ae[aa].getValueCount() > 1)
{
- Cache.log.warn("ignoring additional "
- + (ae[aa].getValueCount() - 1)
- + " values in annotation element.");
+ Console.warn(
+ "ignoring additional " + (ae[aa].getValueCount() - 1)
+ + " values in annotation element.");
}
val = ae[aa].getValue(0);
}
if (colour == null)
{
anot[row][pos] = new jalview.datamodel.Annotation(
- (dc != null) ? dc : "", desc, (ss != null) ? ss
- .charAt(0) : ' ', val);
+ (dc != null) ? dc : "", desc,
+ (ss != null) ? ss.charAt(0) : ' ', val);
}
else
{
anot[row][pos] = new jalview.datamodel.Annotation(
- (dc != null) ? dc : "", desc, (ss != null) ? ss
- .charAt(0) : ' ', val, colour);
+ (dc != null) ? dc : "", desc,
+ (ss != null) ? ss.charAt(0) : ' ', val, colour);
}
}
else
{
- Cache.log.warn("Ignoring out of bound annotation element " + aa
+ Console.warn("Ignoring out of bound annotation element " + aa
+ " in " + annotation.getVorbaId().getId());
}
}
@@ -2118,24 +2184,21 @@ public class VamsasAppDatastore
anot[1][i].description = anot[1][i].description + " (after)";
}
}
- return new Object[]
- { AeContent, rangeMap, anot[0], anot[1] };
+ return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
}
else
{
// no annotations to parse. Just return an empty annotationElement[]
// array.
- return new Object[]
- { AeContent, rangeMap, anot[0], anot[1] };
+ return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
}
// return null;
}
/**
* @param jal
- * the jalview alignment to which the annotation will be
- * attached (ideally - freshly updated from corresponding
- * vamsas alignment)
+ * the jalview alignment to which the annotation will be attached
+ * (ideally - freshly updated from corresponding vamsas alignment)
* @param annotation
* @return unbound jalview alignment annotation object.
*/
@@ -2182,25 +2245,30 @@ public class VamsasAppDatastore
Float val = null;
try
{
- val = new Float(props[p].getContent());
+ val = Float.valueOf(props[p].getContent());
} catch (Exception e)
{
- Cache.log.warn("Failed to parse threshold property");
+ Console.warn("Failed to parse threshold property");
}
if (val != null)
+ {
if (gl == null)
{
- gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
+ gl = new GraphLine(val.floatValue(), "",
+ java.awt.Color.black);
}
else
{
gl.value = val.floatValue();
}
+ }
}
else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name"))
{
if (gl == null)
+ {
gl = new GraphLine(0, "", java.awt.Color.black);
+ }
gl.label = props[p].getContent();
}
}
@@ -2220,14 +2288,14 @@ public class VamsasAppDatastore
}
if (parsedRangeAnnotation == null)
{
- Cache.log
- .debug("Inserting empty annotation row elements for a whole-alignment annotation.");
+ Console.debug(
+ "Inserting empty annotation row elements for a whole-alignment annotation.");
}
else
{
if (parsedRangeAnnotation[3] != null)
{
- Cache.log.warn("Ignoring 'After' annotation row in "
+ Console.warn("Ignoring 'After' annotation row in "
+ annotation.getVorbaId());
}
jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
@@ -2236,11 +2304,12 @@ public class VamsasAppDatastore
// way its 'odd' - there is already an existing TODO about removing this
// flag as being redundant
/*
- * if
- * ((annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class) &&
- * ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph()) ||
- * (hasSequenceRef=true &&
- * ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {
+ * if((annotation.getClass().equals(uk.ac.vamsas.objects.core.
+ * AlignmentAnnotation.class) &&
+ * ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
+ * || (hasSequenceRef=true &&
+ * ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
+ * )annotation).getGraph())) {
*/
if (has[HASVALS])
{
@@ -2314,7 +2383,8 @@ public class VamsasAppDatastore
&& arow[i].description.length() < 3)
{
// copy over the description as the display char.
- arow[i].displayCharacter = new String(arow[i].description);
+ arow[i].displayCharacter = new String(
+ arow[i].description);
}
}
else
@@ -2345,7 +2415,7 @@ public class VamsasAppDatastore
}
if (annotation.getLinkCount() > 0)
{
- Cache.log.warn("Ignoring " + annotation.getLinkCount()
+ Console.warn("Ignoring " + annotation.getLinkCount()
+ "links added to AlignmentAnnotation.");
}
if (annotation.getModifiable() == null
@@ -2370,8 +2440,8 @@ public class VamsasAppDatastore
}
} catch (Exception e)
{
- Cache.log
- .info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
+ Console.info(
+ "UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
}
return jan;
@@ -2380,7 +2450,6 @@ public class VamsasAppDatastore
return null;
}
-
/**
* get real bounds of a RangeType's specification. start and end are an
* inclusive range within which all segments and positions lie. TODO: refactor
@@ -2396,8 +2465,8 @@ public class VamsasAppDatastore
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString(
+ "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
@@ -2420,8 +2489,7 @@ public class VamsasAppDatastore
// could do a polarity for pos range too. and pass back indication of
// discontinuities.
int pos = dseta.getPos(0).getI();
- se = new int[]
- { pos, pos };
+ se = new int[] { pos, pos };
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
@@ -2455,8 +2523,8 @@ public class VamsasAppDatastore
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString(
+ "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
@@ -2466,7 +2534,7 @@ public class VamsasAppDatastore
int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
{
- posList.add(new Integer(p));
+ posList.add(Integer.valueOf(p));
}
}
}
@@ -2477,7 +2545,7 @@ public class VamsasAppDatastore
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
- posList.add(new Integer(pos));
+ posList.add(Integer.valueOf(pos));
}
}
}
@@ -2497,12 +2565,12 @@ public class VamsasAppDatastore
/**
*
* @param maprange
- * where the from range is the local mapped range, and the to
- * range is the 'mapped' range in the MapRangeType
+ * where the from range is the local mapped range, and the to range
+ * is the 'mapped' range in the MapRangeType
* @param default
- * unit for local
+ * unit for local
* @param default
- * unit for mapped
+ * unit for mapped
* @return MapList
*/
private jalview.util.MapList parsemapType(MapType maprange, int localu,
@@ -2513,8 +2581,9 @@ public class VamsasAppDatastore
int[] mappedRange = getMapping(maprange.getMapped());
long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
: localu;
- long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
- .getUnit() : mappedu;
+ long mu = maprange.getMapped().hasUnit()
+ ? maprange.getMapped().getUnit()
+ : mappedu;
ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
(int) mu);
return ml;
@@ -2524,15 +2593,15 @@ public class VamsasAppDatastore
* initialise a range type object from a set of start/end inclusive intervals
*
* @param mrt
- * @param range
+ * @param ranges
*/
- private void initRangeType(RangeType mrt, int[] range)
+ private void initRangeType(RangeType mrt, List ranges)
{
- for (int i = 0; i < range.length; i += 2)
+ for (int[] range : ranges)
{
Seg vSeg = new Seg();
- vSeg.setStart(range[i]);
- vSeg.setEnd(range[i + 1]);
+ vSeg.setStart(range[0]);
+ vSeg.setEnd(range[1]);
mrt.addSeg(vSeg);
}
}
@@ -2567,8 +2636,8 @@ public class VamsasAppDatastore
*
* if (jprov != null) { entries = jprov.getEntries(); for (int i = 0; i <
* entries.length; i++) { provEntry = new Entry(); try { date = new
- * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex) {
- * ex.printStackTrace();
+ * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex)
+ * { ex.printStackTrace();
*
* date = new org.exolab.castor.types.Date(entries[i].getDate()); }
* provEntry.setDate(date); provEntry.setUser(entries[i].getUser());
@@ -2586,9 +2655,9 @@ public class VamsasAppDatastore
jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
for (int i = 0; i < prov.getEntryCount(); i++)
{
- jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i)
- .getAction(), prov.getEntry(i).getDate(), prov.getEntry(i)
- .getId());
+ jprov.addEntry(prov.getEntry(i).getUser(),
+ prov.getEntry(i).getAction(), prov.getEntry(i).getDate(),
+ prov.getEntry(i).getId());
}
return jprov;
@@ -2655,10 +2724,10 @@ public class VamsasAppDatastore
return vobj2jv;
}
- public void storeSequenceMappings(AlignViewport viewport, String title)
- throws Exception
+ public void storeSequenceMappings(AlignmentViewport viewport,
+ String title) throws Exception
{
- AlignViewport av = viewport;
+ AlignmentViewport av = viewport;
try
{
jalview.datamodel.AlignmentI jal = av.getAlignment();
@@ -2667,42 +2736,42 @@ public class VamsasAppDatastore
DataSet dataset = null;
if (jal.getDataset() == null)
{
- Cache.log.warn("Creating new dataset for an alignment.");
+ Console.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
}
- dataset = (DataSet) ((Alignment) getjv2vObj(viewport.getSequenceSetId())).getV_parent(); // jal.getDataset());
- if (dataset==null)
+ dataset = (DataSet) ((Alignment) getjv2vObj(
+ viewport.getSequenceSetId())).getV_parent(); // jal.getDataset());
+ if (dataset == null)
{
dataset = (DataSet) getjv2vObj(jal.getDataset());
- Cache.log.error("Can't find the correct dataset for the alignment in this view. Creating new one.");
+ Console.error(
+ "Can't find the correct dataset for the alignment in this view. Creating new one.");
}
// Store any sequence mappings.
- if (av.getAlignment().getCodonFrames() != null
- && av.getAlignment().getCodonFrames().length > 0)
+ List cframes = av.getAlignment().getCodonFrames();
+ if (cframes != null)
{
- jalview.datamodel.AlignedCodonFrame[] cframes = av.getAlignment()
- .getCodonFrames();
- for (int cf = 0; cf < cframes.length; cf++)
+ for (AlignedCodonFrame acf : cframes)
{
- if (cframes[cf].getdnaSeqs()!=null && cframes[cf].getdnaSeqs().length > 0)
+ if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0)
{
- jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs();
- jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings();
+ jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs();
+ jalview.datamodel.Mapping[] mps = acf.getProtMappings();
for (int smp = 0; smp < mps.length; smp++)
{
- uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]);
+ uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(
+ dmps[smp]);
if (mfrom != null)
{
- new jalview.io.vamsas.Sequencemapping(this, mps[smp],
- mfrom, dataset);
+ new jalview.io.vamsas.Sequencemapping(this, mps[smp], mfrom,
+ dataset);
}
else
{
- Cache.log
- .warn("NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
- + dmps[smp].getDisplayId(true)
- + " to "
+ Console.warn(
+ "NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
+ + dmps[smp].getDisplayId(true) + " to "
+ mps[smp].getTo().getName());
}
}
@@ -2711,8 +2780,9 @@ public class VamsasAppDatastore
}
} catch (Exception e)
{
- throw new Exception("Couldn't store sequence mappings for " + title,
- e);
+ throw new Exception(MessageManager.formatMessage(
+ "exception.couldnt_store_sequence_mappings", new String[]
+ { title }), e);
}
}
@@ -2733,19 +2803,22 @@ public class VamsasAppDatastore
}
/**
- * @param skipList the skipList to set
+ * @param skipList
+ * the skipList to set
*/
public void setSkipList(Hashtable skipList)
{
this.skipList = skipList;
}
+
/**
* registry for datastoreItems
*/
DatastoreRegistry dsReg = new DatastoreRegistry();
+
public DatastoreRegistry getDatastoreRegisty()
{
- if (dsReg==null)
+ if (dsReg == null)
{
dsReg = new DatastoreRegistry();
}