X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=d5801296ed3a0df7b410c2dfda1cf89297bcd22b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=64e40e35690ae2d7e20806216077dc258c990110;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 64e40e3..d580129 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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;
@@ -30,6 +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.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
import java.io.IOException;
import java.util.Enumeration;
import java.util.HashMap;
@@ -37,12 +43,35 @@ import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
import java.util.List;
+import java.util.Set;
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;
/*
@@ -122,7 +151,7 @@ public class VamsasAppDatastore
private void buildSkipList()
{
skipList = new Hashtable();
- AlignFrame[] al = Desktop.getAlignframes();
+ AlignFrame[] al = Desktop.getAlignFrames();
for (int f = 0; al != null && f < al.length; f++)
{
skipList.put(al[f].getViewport().getSequenceSetId(), al[f]);
@@ -217,10 +246,12 @@ public class VamsasAppDatastore
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
- "Warning? Overwriting existing vamsas id binding for "
- + vobj.getVorbaId(), new Exception(
- "Overwriting vamsas id binding."));
+ Cache.log
+ .debug("Warning? Overwriting existing vamsas id binding for "
+ + vobj.getVorbaId(),
+ new Exception(
+ MessageManager
+ .getString("exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
@@ -308,7 +339,8 @@ public class VamsasAppDatastore
&& 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.");
+ MessageManager
+ .getString("error.implementation_error_cannot_map_alignment_sequences"));
// This occurs because the dataset for the alignment we are
// trying to
}
@@ -725,12 +757,12 @@ public class VamsasAppDatastore
* @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)
{
@@ -1065,8 +1097,10 @@ public class VamsasAppDatastore
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));
+ }
}
((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
bindjvvobj(alan, an);
@@ -1229,8 +1263,7 @@ public class VamsasAppDatastore
end = start;
start = t;
}
- return new int[]
- { start, end, pol < 0 ? 1 : 0 };
+ return new int[] { start, end, pol < 0 ? 1 : 0 };
}
/**
@@ -1301,7 +1334,7 @@ public class VamsasAppDatastore
};
if (dojvsync)
{
- fromxml.LoadJalviewAlign(jprovider);
+ fromxml.loadJalviewAlign(jprovider);
}
} catch (Exception e)
{
@@ -1349,7 +1382,7 @@ public class VamsasAppDatastore
};
if (dojvsync)
{
- fromxml.LoadJalviewAlign(jarstream);
+ fromxml.loadJalviewAlign(jarstream);
}
} catch (Exception e)
{
@@ -1378,12 +1411,12 @@ public class VamsasAppDatastore
// sync,
// and if any contain more than one view, then remove the one generated by
// document update.
- AlignViewport views[], av = null;
+ AlignmentViewport views[], av = null;
AlignFrame af = null;
Iterator newviews = newAlignmentViews.iterator();
while (newviews.hasNext())
{
- av = (AlignViewport) newviews.next();
+ av = (AlignmentViewport) newviews.next();
af = Desktop.getAlignFrameFor(av);
// TODO implement this : af.getNumberOfViews
String seqsetidobj = av.getSequenceSetId();
@@ -1400,7 +1433,8 @@ public class VamsasAppDatastore
// to the align frames.
boolean gathered = false;
String newviewid = null;
- AlignedCodonFrame[] mappings = av.getAlignment().getCodonFrames();
+ Set mappings = av.getAlignment()
+ .getCodonFrames();
for (int i = 0; i < views.length; i++)
{
if (views[i] != av)
@@ -1435,11 +1469,11 @@ 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(Desktop.instance)
- .addMappings(mappings);
+ .registerMappings(mappings);
}
}
}
@@ -1470,9 +1504,9 @@ public class VamsasAppDatastore
{
// NOTE: this happens if user deletes object in one session then updates
// from another client
- throw new Error(
- "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
- + oldjvobject + ")");
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_old_jalview_object_not_bound",
+ new String[] { oldjvobject.toString() }));
}
if (newjvobject != null)
{
@@ -1497,7 +1531,7 @@ public class VamsasAppDatastore
jxml.setSkipList(skipList);
if (dojvsync)
{
- jxml.SaveState(new JarOutputStream(cappdata
+ jxml.saveState(new JarOutputStream(cappdata
.getClientOutputStream()));
}
@@ -1681,7 +1715,7 @@ public class VamsasAppDatastore
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)
@@ -1955,10 +1989,10 @@ 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)
{
@@ -2001,8 +2035,7 @@ 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],
@@ -2137,15 +2170,13 @@ 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;
}
@@ -2206,6 +2237,7 @@ public class VamsasAppDatastore
Cache.log.warn("Failed to parse threshold property");
}
if (val != null)
+ {
if (gl == null)
{
gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
@@ -2214,11 +2246,14 @@ public class VamsasAppDatastore
{
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();
}
}
@@ -2415,7 +2450,8 @@ public class VamsasAppDatastore
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
@@ -2438,8 +2474,7 @@ 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();
@@ -2474,7 +2509,8 @@ public class VamsasAppDatastore
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
@@ -2540,15 +2576,15 @@ 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);
}
}
@@ -2671,10 +2707,10 @@ public class VamsasAppDatastore
return vobj2jv;
}
- public void storeSequenceMappings(AlignViewport viewport, String title)
+ public void storeSequenceMappings(AlignmentViewport viewport, String title)
throws Exception
{
- AlignViewport av = viewport;
+ AlignmentViewport av = viewport;
try
{
jalview.datamodel.AlignmentI jal = av.getAlignment();
@@ -2696,18 +2732,15 @@ public class VamsasAppDatastore
}
// Store any sequence mappings.
- if (av.getAlignment().getCodonFrames() != null
- && av.getAlignment().getCodonFrames().length > 0)
+ Set 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]);
@@ -2730,8 +2763,9 @@ 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);
}
}