X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=58adfb2f4ba3ea9e62d60ec2a149c2dafc3bcff9;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=82282395155218814d5df433e13c33d03947d858;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 8228239..58adfb2 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,30 +1,29 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import jalview.bin.Cache;
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;
@@ -34,7 +33,7 @@ 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.util.MessageManager;
import java.io.IOException;
import java.util.Enumeration;
@@ -42,6 +41,7 @@ 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;
@@ -51,14 +51,14 @@ import uk.ac.vamsas.objects.core.*;
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
{
@@ -224,8 +224,7 @@ public class VamsasAppDatastore
{
Cache.log.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()))
@@ -312,8 +311,7 @@ public class VamsasAppDatastore
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.");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_map_alignment_sequences"));
// This occurs because the dataset for the alignment we are
// trying to
}
@@ -546,12 +544,8 @@ 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)
@@ -884,7 +878,7 @@ 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;
@@ -1260,7 +1254,7 @@ public class VamsasAppDatastore
/**
* list of alignment views created when updating Jalview from document.
*/
- private Vector newAlignmentViews = new Vector();
+ private final Vector newAlignmentViews = new Vector();
/**
* update local jalview view settings from the stored appdata (if any)
@@ -1292,6 +1286,7 @@ public class VamsasAppDatastore
jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
{
+ @Override
public String getFilename()
{
@@ -1299,6 +1294,7 @@ public class VamsasAppDatastore
return "Jalview Vamsas Document Client Data";
}
+ @Override
public JarInputStream getJarInputStream() throws IOException
{
jalview.bin.Cache.log
@@ -1308,7 +1304,7 @@ public class VamsasAppDatastore
};
if (dojvsync)
{
- fromxml.LoadJalviewAlign(jprovider);
+ fromxml.loadJalviewAlign(jprovider);
}
} catch (Exception e)
{
@@ -1338,6 +1334,7 @@ public class VamsasAppDatastore
jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
{
+ @Override
public String getFilename()
{
@@ -1345,6 +1342,7 @@ public class VamsasAppDatastore
return "Jalview Vamsas Document User Data";
}
+ @Override
public JarInputStream getJarInputStream() throws IOException
{
jalview.bin.Cache.log
@@ -1354,7 +1352,7 @@ public class VamsasAppDatastore
};
if (dojvsync)
{
- fromxml.LoadJalviewAlign(jarstream);
+ fromxml.loadJalviewAlign(jarstream);
}
} catch (Exception e)
{
@@ -1443,7 +1441,8 @@ public class VamsasAppDatastore
if (mappings != null && mappings.length > 0)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).addMappings(mappings);
+ .getStructureSelectionManager(Desktop.instance)
+ .addMappings(mappings);
}
}
}
@@ -1472,9 +1471,9 @@ public class VamsasAppDatastore
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)
{
@@ -1499,7 +1498,7 @@ public class VamsasAppDatastore
jxml.setSkipList(skipList);
if (dojvsync)
{
- jxml.SaveState(new JarOutputStream(cappdata
+ jxml.saveState(new JarOutputStream(cappdata
.getClientOutputStream()));
}
@@ -1573,7 +1572,7 @@ public class VamsasAppDatastore
// ///LOAD DATASET
DataSet dataset = root.getDataSet(_ds);
int i, iSize = dataset.getSequenceCount();
- Vector dsseqs;
+ List dsseqs;
jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
int jremain = 0;
if (jdataset == null)
@@ -1620,8 +1619,8 @@ 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.");
@@ -1782,8 +1781,8 @@ 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 "
@@ -2416,8 +2415,7 @@ 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)
{
@@ -2475,8 +2473,7 @@ 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)
{
@@ -2732,8 +2729,7 @@ 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);
}
}