X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=2a6b601989f0891832c836401d8be1ca8c072bee;hb=f52f7b378972cc884b5d3e5cc250f89667f558f7;hp=0514fb89013eca8926704c7c48ca36181edf61fa;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 0514fb8..2a6b601 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,278 +1,286 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
- */
-
-package jalview.datamodel;
-
-import java.util.*;
-
-public class HiddenSequences
-{
- public SequenceI[] hiddenSequences;
- AlignmentI alignment;
-
- public HiddenSequences(AlignmentI al)
- {
- alignment = al;
- }
-
- public int getSize()
- {
- if (hiddenSequences == null)
- {
- return 0;
- }
- int count = 0;
- for (int i = 0; i < hiddenSequences.length; i++)
- {
- if (hiddenSequences[i] != null)
- {
- count++;
- }
- }
-
- return count;
- }
-
- public int getWidth()
- {
- int width = 0;
- for (int i = 0; i < hiddenSequences.length; i++)
- {
- if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width)
- {
- width = hiddenSequences[i].getLength();
- }
- }
-
- return width;
- }
-
- /**
- * Call this method if sequences are removed from the
- * main alignment
- */
- public void adjustHeightSequenceDeleted(int seqIndex)
- {
- if (hiddenSequences == null)
- {
- return;
- }
-
- int alHeight = alignment.getHeight();
-
- SequenceI[] tmp = new SequenceI[alHeight + getSize()];
- int deletionIndex = adjustForHiddenSeqs(seqIndex);
-
- for (int i = 0; i < hiddenSequences.length; i++)
- {
- if (hiddenSequences[i] == null)
- {
- continue;
- }
-
- if (i > deletionIndex)
- {
- tmp[i - 1] = hiddenSequences[i];
- }
- else
- {
- tmp[i] = hiddenSequences[i];
- }
- }
-
- hiddenSequences = tmp;
-
- }
-
- /**
- * Call this method if sequences are added to or removed from the
- * main alignment
- */
- public void adjustHeightSequenceAdded()
- {
- if (hiddenSequences == null)
- {
- return;
- }
-
- int alHeight = alignment.getHeight();
-
- SequenceI[] tmp = new SequenceI[alHeight + getSize()];
- System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length);
- hiddenSequences = tmp;
- }
-
- public void hideSequence(SequenceI sequence)
- {
- if (hiddenSequences == null)
- {
- hiddenSequences = new SequenceI[alignment.getHeight()];
- }
-
- int alignmentIndex = alignment.findIndex(sequence);
- alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
-
- if (hiddenSequences[alignmentIndex] != null)
- {
- System.out.println("ERROR!!!!!!!!!!!");
- }
-
- hiddenSequences[alignmentIndex] = sequence;
-
- alignment.deleteSequence(sequence);
- }
-
- public Vector showAll(Hashtable hiddenReps)
- {
- Vector revealedSeqs = new Vector();
- for (int i = 0; i < hiddenSequences.length; i++)
- {
- if (hiddenSequences[i] != null)
- {
- Vector tmp = showSequence(i, hiddenReps);
- for (int t = 0; t < tmp.size(); t++)
- {
- revealedSeqs.addElement(tmp.elementAt(t));
- }
- }
- }
- return revealedSeqs;
- }
-
- public Vector showSequence(int alignmentIndex, Hashtable hiddenReps)
- {
- Vector revealedSeqs = new Vector();
- SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
- if (repSequence != null &&
- hiddenReps != null
- && hiddenReps.containsKey(repSequence))
- {
- hiddenReps.remove(repSequence);
- revealedSeqs.addElement(repSequence);
- }
-
- int start = adjustForHiddenSeqs(alignmentIndex - 1);
- int end = adjustForHiddenSeqs(alignmentIndex);
- if (end >= hiddenSequences.length)
- {
- end = hiddenSequences.length - 1;
- }
-
- for (int index = end; index > start; index--)
- {
- SequenceI seq = hiddenSequences[index];
- hiddenSequences[index] = null;
-
- if (seq != null)
- {
- if (seq.getLength() > 0)
- {
- revealedSeqs.addElement(seq);
- alignment.getSequences().insertElementAt(seq, alignmentIndex);
- }
- else
- {
- System.out.println(seq.getName() + " has been deleted whilst hidden");
- }
- }
-
- }
-
- return revealedSeqs;
- }
-
- public SequenceI getHiddenSequence(int alignmentIndex)
- {
- return hiddenSequences[alignmentIndex];
- }
-
- public int findIndexWithoutHiddenSeqs(int alignmentIndex)
- {
- int index = 0;
- int hiddenSeqs = 0;
- if (hiddenSequences.length <= alignmentIndex)
- {
- alignmentIndex = hiddenSequences.length - 1;
- }
-
- while (index <= alignmentIndex)
- {
- if (hiddenSequences[index] != null)
- {
- hiddenSeqs++;
- }
- index++;
- }
- ;
-
- return (alignmentIndex - hiddenSeqs);
- }
-
- public int adjustForHiddenSeqs(int alignmentIndex)
- {
- int index = 0;
- int hSize = hiddenSequences.length;
- while (index <= alignmentIndex && index < hSize)
- {
- if (hiddenSequences[index] != null)
- {
- alignmentIndex++;
- }
- index++;
- }
- ;
-
- return alignmentIndex;
- }
-
- public AlignmentI getFullAlignment()
- {
- int isize = hiddenSequences.length;
- SequenceI[] seq = new Sequence[isize];
-
- int index = 0;
- for (int i = 0; i < hiddenSequences.length; i++)
- {
- if (hiddenSequences[i] != null)
- {
- seq[i] = hiddenSequences[i];
- }
- else
- {
- seq[i] = alignment.getSequenceAt(index);
- index++;
- }
- }
-
- return new Alignment(seq);
- }
-
- public boolean isHidden(SequenceI seq)
- {
- for (int i = 0; i < hiddenSequences.length; i++)
- {
- if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
- {
- return true;
- }
- }
-
- return false;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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 .
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+public class HiddenSequences
+{
+ /**
+ * holds a list of hidden sequences associated with an alignment.
+ */
+ public SequenceI[] hiddenSequences;
+
+ AlignmentI alignment;
+
+ public HiddenSequences(AlignmentI al)
+ {
+ alignment = al;
+ }
+
+ public int getSize()
+ {
+ if (hiddenSequences == null)
+ {
+ return 0;
+ }
+ int count = 0;
+ for (int i = 0; i < hiddenSequences.length; i++)
+ {
+ if (hiddenSequences[i] != null)
+ {
+ count++;
+ }
+ }
+
+ return count;
+ }
+
+ public int getWidth()
+ {
+ int width = 0;
+ for (int i = 0; i < hiddenSequences.length; i++)
+ {
+ if (hiddenSequences[i] != null
+ && hiddenSequences[i].getLength() > width)
+ {
+ width = hiddenSequences[i].getLength();
+ }
+ }
+
+ return width;
+ }
+
+ /**
+ * Call this method if sequences are removed from the main alignment
+ */
+ public void adjustHeightSequenceDeleted(int seqIndex)
+ {
+ if (hiddenSequences == null)
+ {
+ return;
+ }
+
+ int alHeight = alignment.getHeight();
+
+ SequenceI[] tmp = new SequenceI[alHeight + getSize()];
+ int deletionIndex = adjustForHiddenSeqs(seqIndex);
+
+ for (int i = 0; i < hiddenSequences.length; i++)
+ {
+ if (hiddenSequences[i] == null)
+ {
+ continue;
+ }
+
+ if (i > deletionIndex)
+ {
+ tmp[i - 1] = hiddenSequences[i];
+ }
+ else
+ {
+ tmp[i] = hiddenSequences[i];
+ }
+ }
+
+ hiddenSequences = tmp;
+
+ }
+
+ /**
+ * Call this method if sequences are added to or removed from the main
+ * alignment
+ */
+ public void adjustHeightSequenceAdded()
+ {
+ if (hiddenSequences == null)
+ {
+ return;
+ }
+
+ int alHeight = alignment.getHeight();
+
+ SequenceI[] tmp = new SequenceI[alHeight + getSize()];
+ System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length);
+ hiddenSequences = tmp;
+ }
+
+ public void hideSequence(SequenceI sequence)
+ {
+ if (hiddenSequences == null)
+ {
+ hiddenSequences = new SequenceI[alignment.getHeight()];
+ }
+
+ int alignmentIndex = alignment.findIndex(sequence);
+ alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
+
+ if (hiddenSequences[alignmentIndex] != null)
+ {
+ System.out.println("ERROR!!!!!!!!!!!");
+ }
+
+ hiddenSequences[alignmentIndex] = sequence;
+
+ alignment.deleteSequence(sequence);
+ }
+
+ public Vector showAll(
+ Map hiddenRepSequences)
+ {
+ Vector revealedSeqs = new Vector();
+ for (int i = 0; i < hiddenSequences.length; i++)
+ {
+ if (hiddenSequences[i] != null)
+ {
+ Vector tmp = showSequence(i, hiddenRepSequences);
+ for (int t = 0; t < tmp.size(); t++)
+ {
+ revealedSeqs.addElement(tmp.elementAt(t));
+ }
+ }
+ }
+ return revealedSeqs;
+ }
+
+ public Vector showSequence(int alignmentIndex,
+ Map hiddenRepSequences)
+ {
+ Vector revealedSeqs = new Vector();
+ SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
+ if (repSequence != null && hiddenRepSequences != null
+ && hiddenRepSequences.containsKey(repSequence))
+ {
+ hiddenRepSequences.remove(repSequence);
+ revealedSeqs.addElement(repSequence);
+ }
+
+ int start = adjustForHiddenSeqs(alignmentIndex - 1);
+ int end = adjustForHiddenSeqs(alignmentIndex);
+ if (end >= hiddenSequences.length)
+ {
+ end = hiddenSequences.length - 1;
+ }
+
+ List asequences;
+ synchronized (asequences = alignment.getSequences())
+ {
+ for (int index = end; index > start; index--)
+ {
+ SequenceI seq = hiddenSequences[index];
+ hiddenSequences[index] = null;
+
+ if (seq != null)
+ {
+ if (seq.getLength() > 0)
+ {
+ revealedSeqs.addElement(seq);
+ asequences.add(alignmentIndex, seq);
+ }
+ else
+ {
+ System.out.println(seq.getName()
+ + " has been deleted whilst hidden");
+ }
+ }
+
+ }
+ }
+
+ return revealedSeqs;
+ }
+
+ public SequenceI getHiddenSequence(int alignmentIndex)
+ {
+ return hiddenSequences[alignmentIndex];
+ }
+
+ public int findIndexWithoutHiddenSeqs(int alignmentIndex)
+ {
+ int index = 0;
+ int hiddenSeqs = 0;
+ if (hiddenSequences.length <= alignmentIndex)
+ {
+ alignmentIndex = hiddenSequences.length - 1;
+ }
+
+ while (index <= alignmentIndex)
+ {
+ if (hiddenSequences[index] != null)
+ {
+ hiddenSeqs++;
+ }
+ index++;
+ }
+ ;
+
+ return (alignmentIndex - hiddenSeqs);
+ }
+
+ public int adjustForHiddenSeqs(int alignmentIndex)
+ {
+ int index = 0;
+ int hSize = hiddenSequences.length;
+ while (index <= alignmentIndex && index < hSize)
+ {
+ if (hiddenSequences[index] != null)
+ {
+ alignmentIndex++;
+ }
+ index++;
+ }
+ ;
+
+ return alignmentIndex;
+ }
+
+ public AlignmentI getFullAlignment()
+ {
+ int isize = hiddenSequences.length;
+ SequenceI[] seq = new Sequence[isize];
+
+ int index = 0;
+ for (int i = 0; i < hiddenSequences.length; i++)
+ {
+ if (hiddenSequences[i] != null)
+ {
+ seq[i] = hiddenSequences[i];
+ }
+ else
+ {
+ seq[i] = alignment.getSequenceAt(index);
+ index++;
+ }
+ }
+
+ return new Alignment(seq);
+ }
+
+ public boolean isHidden(SequenceI seq)
+ {
+ for (int i = 0; i < hiddenSequences.length; i++)
+ {
+ if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+ {
+ return true;
+ }
+ }
+
+ return false;
+ }
+}