X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=e7c9316909d12e04d958166f1f309881a3056b1e;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=c5019d1aec59e94643326637f47377798c8a572d;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index c5019d1..e7c9316 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,27 +1,30 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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.datamodel;
+import jalview.util.MessageManager;
import jalview.util.ShiftList;
import java.io.PrintStream;
-import java.util.Enumeration;
+import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
@@ -44,11 +47,13 @@ public class AlignmentView
* one or more ScGroup objects, which are referenced by each seqCigar's group
* membership
*/
- private Vector scGroups;
+ private List scGroups = null;
+
+ private boolean isNa = false;
- private boolean isNa=false;
/**
* false if the view concerns peptides
+ *
* @return
*/
public boolean isNa()
@@ -128,27 +133,24 @@ public class AlignmentView
selseqs = alignment.getSequencesArray();
}
+ List> seqsets = new ArrayList>();
// get the alignment's group list and make a copy
- Vector grps = new Vector();
+ List grps = new ArrayList();
List gg = alignment.getGroups();
grps.addAll(gg);
ScGroup[] sgrps = null;
boolean addedgps[] = null;
if (grps != null)
{
- SequenceGroup sg;
if (selection != null && selectedRegionOnly)
{
// trim annotation to the region being stored.
// strip out any groups that do not actually intersect with the
// visible and selected region
int ssel = selection.getStartRes(), esel = selection.getEndRes();
- Vector isg = new Vector();
- Enumeration en = grps.elements();
- while (en.hasMoreElements())
+ List isg = new ArrayList();
+ for (SequenceGroup sg : grps)
{
- sg = (SequenceGroup) en.nextElement();
-
if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel))
{
// adjust bounds of new group, if necessary.
@@ -163,7 +165,7 @@ public class AlignmentView
sg.setStartRes(sg.getStartRes() - ssel + 1);
sg.setEndRes(sg.getEndRes() - ssel + 1);
- isg.addElement(sg);
+ isg.add(sg);
}
}
grps = isg;
@@ -173,13 +175,15 @@ public class AlignmentView
addedgps = new boolean[grps.size()];
for (int g = 0; g < sgrps.length; g++)
{
- sg = (SequenceGroup) grps.elementAt(g);
+ SequenceGroup sg = grps.get(g);
sgrps[g] = new ScGroup();
sgrps[g].sg = new SequenceGroup(sg);
addedgps[g] = false;
- grps.setElementAt(sg.getSequences(null), g);
+ // can't set entry 0 in an empty list
+ // seqsets.set(g, sg.getSequences(null));
+ seqsets.add(sg.getSequences());
}
- // grps now contains vectors (should be sets) for each group, so we can
+ // seqsets now contains vectors (should be sets) for each group, so we can
// track when we've done with the group
}
int csi = 0;
@@ -193,11 +197,11 @@ public class AlignmentView
sequences[csi].setGroupMembership(selected);
selected.addElement(sequences[csi]);
}
- if (grps != null)
+ if (seqsets != null)
{
for (int sg = 0; sg < sgrps.length; sg++)
{
- if (((Vector) grps.elementAt(sg)).contains(selseqs[i]))
+ if ((seqsets.get(sg)).contains(selseqs[i]))
{
sequences[csi].setGroupMembership(sgrps[sg]);
sgrps[sg].sg.deleteSequence(selseqs[i], false);
@@ -206,10 +210,10 @@ public class AlignmentView
{
if (scGroups == null)
{
- scGroups = new Vector();
+ scGroups = new ArrayList();
}
addedgps[sg] = true;
- scGroups.addElement(sgrps[sg]);
+ scGroups.add(sgrps[sg]);
}
}
}
@@ -238,7 +242,8 @@ public class AlignmentView
if (!seqcigararray.isSeqCigarArray())
{
throw new Error(
- "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
+ MessageManager
+ .getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
}
// contigs = seqcigararray.applyDeletions();
contigs = seqcigararray.getDeletedRegions();
@@ -295,8 +300,7 @@ public class AlignmentView
{
ColumnSelection colsel = new ColumnSelection();
- return new Object[]
- {
+ return new Object[] {
SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
contigs), colsel };
}
@@ -352,7 +356,7 @@ public class AlignmentView
SequenceGroup[] nsg = new SequenceGroup[nvg];
for (int g = 0; g < nvg; g++)
{
- SequenceGroup sg = ((ScGroup) scGroups.elementAt(g)).sg;
+ SequenceGroup sg = scGroups.get(g).sg;
if (r)
{
if (sg.getStartRes() > gend || sg.getEndRes() < gstart)
@@ -438,7 +442,7 @@ public class AlignmentView
for (int g = 0; g < nvg; g++)
{
if (nsg[g] != null
- && sequences[nsq].isMemberOf(scGroups.elementAt(g)))
+ && sequences[nsq].isMemberOf(scGroups.get(g)))
{
nsg[g].addSequence(aln[nsq], false);
}
@@ -462,6 +466,7 @@ public class AlignmentView
* alignment.
*
* @param c
+ * gap character to use to recreate the alignment
* @return
*/
private SequenceI[] getVisibleSeqs(char c)
@@ -469,13 +474,9 @@ public class AlignmentView
SequenceI[] aln = new SequenceI[sequences.length];
for (int i = 0, j = sequences.length; i < j; i++)
{
- aln[i] = sequences[i].getSeq('-');
- }
- // Remove hidden regions from sequence objects.
- String seqs[] = getSequenceStrings('-');
- for (int i = 0, j = aln.length; i < j; i++)
- {
- aln[i].setSequence(seqs[i]);
+ aln[i] = sequences[i].getSeq(c);
+ // Remove hidden regions from sequence
+ aln[i].setSequence(getASequenceString(c, i));
}
return aln;
}
@@ -511,8 +512,38 @@ public class AlignmentView
}
/**
+ * build a string excluding hidden regions from a particular sequence in the
+ * view
+ *
+ * @param c
+ * @param n
+ * @return
+ */
+ private String getASequenceString(char c, int n)
+ {
+ String sqn;
+ String fullseq = sequences[n].getSequenceString(c);
+ if (contigs != null)
+ {
+ sqn = "";
+ int p = 0;
+ for (int h = 0; h < contigs.length; h += 3)
+ {
+ sqn += fullseq.substring(p, contigs[h + 1]);
+ p = contigs[h + 1] + contigs[h + 2];
+ }
+ sqn += fullseq.substring(p);
+ }
+ else
+ {
+ sqn = fullseq;
+ }
+ return sqn;
+ }
+
+ /**
* get an array of visible sequence strings for a view on an alignment using
- * the given gap character
+ * the given gap character uses getASequenceString
*
* @param c
* char
@@ -523,22 +554,7 @@ public class AlignmentView
String[] seqs = new String[sequences.length];
for (int n = 0; n < sequences.length; n++)
{
- String fullseq = sequences[n].getSequenceString(c);
- if (contigs != null)
- {
- seqs[n] = "";
- int p = 0;
- for (int h = 0; h < contigs.length; h += 3)
- {
- seqs[n] += fullseq.substring(p, contigs[h + 1]);
- p = contigs[h + 1] + contigs[h + 2];
- }
- seqs[n] += fullseq.substring(p);
- }
- else
- {
- seqs[n] = fullseq;
- }
+ seqs[n] = getASequenceString(c, n);
}
return seqs;
}
@@ -648,7 +664,9 @@ public class AlignmentView
{
if (sequences == null || width <= 0)
{
- throw new Error("empty view cannot be updated.");
+ throw new Error(
+ MessageManager
+ .getString("error.empty_view_cannot_be_updated"));
}
if (nvismsa == null)
{
@@ -679,10 +697,16 @@ public class AlignmentView
if (mseq.length != sequences.length)
{
throw new Error(
- "Mismatch between number of sequences in block "
- + j + " (" + mseq.length
- + ") and the original view ("
- + sequences.length + ")");
+ MessageManager
+ .formatMessage(
+ "error.mismatch_between_number_of_sequences_in_block",
+ new String[] {
+ Integer.valueOf(j).toString(),
+ Integer.valueOf(mseq.length)
+ .toString(),
+ Integer.valueOf(
+ sequences.length)
+ .toString() }));
}
swidth = mseq[0].getLength(); // JBPNote: could ensure padded
// here.
@@ -835,27 +859,30 @@ public class AlignmentView
else
{
// place gaps.
- throw new Error("Padding not yet implemented.");
+ throw new Error(
+ MessageManager
+ .getString("error.padding_not_yet_implemented"));
}
}
}
}
}
- return new Object[]
- { alignment, columnselection };
+ return new Object[] { alignment, columnselection };
}
else
{
if (nvismsa.length != 1)
{
throw new Error(
- "Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="
- + nvismsa.length);
+ MessageManager
+ .formatMessage(
+ "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view",
+ new String[] { Integer.valueOf(
+ nvismsa.length).toString() }));
}
if (nvismsa[0] != null)
{
- return new Object[]
- { nvismsa[0], new ColumnSelection() };
+ return new Object[] { nvismsa[0], new ColumnSelection() };
}
else
{
@@ -916,8 +943,7 @@ public class AlignmentView
}
else
{
- return new int[]
- { 0, width };
+ return new int[] { 0, width };
}
}
@@ -1040,7 +1066,7 @@ public class AlignmentView
+ " groups defined on the view.");
for (int g = 0; g < view.scGroups.size(); g++)
{
- ScGroup sgr = (ScGroup) view.scGroups.elementAt(g);
+ ScGroup sgr = view.scGroups.get(g);
os.println("Group " + g + ": Name = " + sgr.sg.getName()
+ " Contains " + sgr.seqs.size() + " Seqs.");
os.println("This group runs from " + sgr.sg.getStartRes() + " to "