X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=b36a0a5066b05bcc8a9d56214b0403c17657d8e4;hb=8e82fa3fbc38ce89f59fde4440830a83bf95289e;hp=6c4cfaea44ecabdc17b643f00a7ed5046675d03b;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java index 6c4cfae..b36a0a5 100644 --- a/src/jalview/datamodel/AlignmentView.java +++ b/src/jalview/datamodel/AlignmentView.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,10 +20,11 @@ */ 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; @@ -46,7 +47,7 @@ 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; @@ -132,27 +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. @@ -167,7 +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; @@ -177,13 +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; @@ -197,11 +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); @@ -210,10 +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]); } } } @@ -241,8 +241,7 @@ public class AlignmentView { if (!seqcigararray.isSeqCigarArray()) { - throw new Error( - "Implementation Error - can only make an alignment view from a CigarArray of sequences."); + throw new Error(MessageManager.getString("error.implementation_error_can_only_make_alignmnet_from_cigararray")); } // contigs = seqcigararray.applyDeletions(); contigs = seqcigararray.getDeletedRegions(); @@ -356,7 +355,7 @@ 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) @@ -442,7 +441,7 @@ 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); } @@ -652,7 +651,7 @@ 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) { @@ -682,11 +681,7 @@ public class AlignmentView j++; if (mseq.length != sequences.length) { - throw new Error( - "Mismatch between number of sequences in block " - + j + " (" + mseq.length - + ") and the original view (" - + sequences.length + ")"); + throw new Error(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. @@ -839,7 +834,7 @@ public class AlignmentView else { // place gaps. - throw new Error("Padding not yet implemented."); + throw new Error(MessageManager.getString("error.padding_not_yet_implemented")); } } } @@ -852,9 +847,7 @@ public class AlignmentView { if (nvismsa.length != 1) { - throw new Error( - "Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks=" - + nvismsa.length); + throw new Error(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) { @@ -1044,7 +1037,7 @@ 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 "