X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=3d848a2a8fb0eecdff5e10738b04ece94791dd77;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=e22042c355e8b27ae7b51d0d48b4a9461ecf2a99;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index e22042c..3d848a2 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,600 +1,1170 @@
-/*
- * 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.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.schemes.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SequenceGroup
-{
- String groupName;
- String description;
- Conservation conserve;
- Vector aaFrequency;
- boolean displayBoxes = true;
- boolean displayText = true;
- boolean colourText = true;
- private Vector sequences = new Vector();
- int width = -1;
-
- /** DOCUMENT ME!! */
- public ColourSchemeI cs;
- int startRes = 0;
- int endRes = 0;
- Color outlineColour = Color.black;
- public int thresholdTextColour = 0;
- public Color textColour = Color.black;
- public Color textColour2 = Color.white;
-
- /**
- * Creates a new SequenceGroup object.
- */
- public SequenceGroup()
- {
- groupName = "JGroup:" + this.hashCode();
- }
-
- /**
- * Creates a new SequenceGroup object.
- *
- * @param sequences DOCUMENT ME!
- * @param groupName DOCUMENT ME!
- * @param scheme DOCUMENT ME!
- * @param displayBoxes DOCUMENT ME!
- * @param displayText DOCUMENT ME!
- * @param colourText DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- */
- public SequenceGroup(Vector sequences, String groupName,
- ColourSchemeI scheme, boolean displayBoxes,
- boolean displayText,
- boolean colourText, int start, int end)
- {
- this.sequences = sequences;
- this.groupName = groupName;
- this.displayBoxes = displayBoxes;
- this.displayText = displayText;
- this.colourText = colourText;
- this.cs = scheme;
- startRes = start;
- endRes = end;
- recalcConservation();
- }
-
- public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
- {
- int iSize = sequences.size();
- SequenceI[] seqs = new SequenceI[iSize];
- SequenceI[] inorder = getSequencesInOrder(align);
-
- for (int i = 0; i < iSize; i++)
- {
- SequenceI seq = inorder[i];
-
- seqs[i] = new Sequence(seq.getName(),
- seq.getSequence(startRes, endRes + 1),
- seq.findPosition(startRes),
- findEndRes(seq));
-
- seqs[i].setDescription(seq.getDescription());
- seqs[i].setDBRef(seq.getDBRef());
- seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
- if (seq.getDatasetSequence() != null)
- {
- seqs[i].setDatasetSequence(seq.getDatasetSequence());
- }
-
- if (seq.getAnnotation() != null)
- {
- for (int a = 0; a < seq.getAnnotation().length; a++)
- {
- seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
- }
- }
- }
-
- return seqs;
-
- }
-
- /**
- * If sequence ends in gaps, the end residue can
- * be correctly calculated here
- * @param seq SequenceI
- * @return int
- */
- public int findEndRes(SequenceI seq)
- {
- int eres = 0;
- char ch;
-
- for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
- {
- ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap( (ch)))
- {
- eres++;
- }
- }
-
- if (eres > 0)
- {
- eres += seq.getStart() - 1;
- }
-
- return eres;
- }
-
- public Vector getSequences(Hashtable hiddenReps)
- {
- if (hiddenReps == null)
- {
- return sequences;
- }
- else
- {
- Vector allSequences = new Vector();
- SequenceI seq, seq2;
- for (int i = 0; i < sequences.size(); i++)
- {
- seq = (SequenceI) sequences.elementAt(i);
- allSequences.addElement(seq);
- if (hiddenReps.containsKey(seq))
- {
- SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
- for (int h = 0; h < hsg.getSize(); h++)
- {
- seq2 = hsg.getSequenceAt(h);
- if (seq2 != seq
- && !allSequences.contains(seq2))
- {
- allSequences.addElement(seq2);
- }
- }
- }
- }
-
- return allSequences;
- }
- }
-
- public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
- {
- Vector tmp = getSequences(hiddenReps);
- if (tmp == null)
- {
- return null;
- }
- SequenceI[] result = new SequenceI[tmp.size()];
- for (int i = 0; i < result.length; i++)
- {
- result[i] = (SequenceI) tmp.elementAt(i);
- }
-
- return result;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param col DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean adjustForRemoveLeft(int col)
- {
- // return value is true if the group still exists
- if (startRes >= col)
- {
- startRes = startRes - col;
- }
-
- if (endRes >= col)
- {
- endRes = endRes - col;
-
- if (startRes > endRes)
- {
- startRes = 0;
- }
- }
- else
- {
- // must delete this group!!
- return false;
- }
-
- return true;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param col DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean adjustForRemoveRight(int col)
- {
- if (startRes > col)
- {
- // delete this group
- return false;
- }
-
- if (endRes >= col)
- {
- endRes = col;
- }
-
- return true;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName()
- {
- return groupName;
- }
-
- public String getDescription()
- {
- return description;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param name DOCUMENT ME!
- */
- public void setName(String name)
- {
- groupName = name;
- }
-
- public void setDescription(String desc)
- {
- description = desc;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Conservation getConservation()
- {
- return conserve;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- */
- public void setConservation(Conservation c)
- {
- conserve = c;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param recalc DOCUMENT ME!
- */
- public void addSequence(SequenceI s, boolean recalc)
- {
- if (s != null && !sequences.contains(s))
- {
- sequences.addElement(s);
- }
-
- if (recalc)
- {
- recalcConservation();
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- public void recalcConservation()
- {
- if (cs == null)
- {
- return;
- }
-
- try
- {
- cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));
-
- if (cs instanceof ClustalxColourScheme)
- {
- ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
- }
-
- if (cs.conservationApplied())
- {
- Conservation c = new Conservation(groupName,
- ResidueProperties.propHash, 3,
- sequences,
- startRes, endRes + 1);
- c.calculate();
- c.verdict(false, 25);
-
- cs.setConservation(c);
-
- if (cs instanceof ClustalxColourScheme)
- {
- ( (ClustalxColourScheme) cs).resetClustalX(sequences,
- getWidth());
- }
- }
- }
- catch (java.lang.OutOfMemoryError err)
- {
- System.out.println("Out of memory loading groups: " + err);
- }
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param recalc DOCUMENT ME!
- */
- public void addOrRemove(SequenceI s, boolean recalc)
- {
- if (sequences.contains(s))
- {
- deleteSequence(s, recalc);
- }
- else
- {
- addSequence(s, recalc);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param recalc DOCUMENT ME!
- */
- public void deleteSequence(SequenceI s, boolean recalc)
- {
- sequences.removeElement(s);
-
- if (recalc)
- {
- recalcConservation();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartRes()
- {
- return startRes;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEndRes()
- {
- return endRes;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void setStartRes(int i)
- {
- startRes = i;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void setEndRes(int i)
- {
- endRes = i;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getSize()
- {
- return sequences.size();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceI getSequenceAt(int i)
- {
- return (SequenceI) sequences.elementAt(i);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setColourText(boolean state)
- {
- colourText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourText()
- {
- return colourText;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setDisplayText(boolean state)
- {
- displayText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getDisplayText()
- {
- return displayText;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setDisplayBoxes(boolean state)
- {
- displayBoxes = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getDisplayBoxes()
- {
- return displayBoxes;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWidth()
- {
- // MC This needs to get reset when characters are inserted and deleted
- if (sequences.size() > 0)
- {
- width = ( (SequenceI) sequences.elementAt(0)).getLength();
- }
-
- for (int i = 1; i < sequences.size(); i++)
- {
- SequenceI seq = (SequenceI) sequences.elementAt(i);
-
- if (seq.getLength() > width)
- {
- width = seq.getLength();
- }
- }
-
- return width;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- */
- public void setOutlineColour(Color c)
- {
- outlineColour = c;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color getOutlineColour()
- {
- return outlineColour;
- }
-
- /**
- *
- * returns the sequences in the group ordered by the ordering given by al
- *
- * @param al Alignment
- * @return SequenceI[]
- */
- public SequenceI[] getSequencesInOrder(AlignmentI al)
- {
- int sSize = sequences.size();
- int alHeight = al.getHeight();
-
- SequenceI[] seqs = new SequenceI[sSize];
-
- int index = 0;
- for (int i = 0; i < alHeight && index < sSize; i++)
- {
- if (sequences.contains(al.getSequenceAt(i)))
- {
- seqs[index++] = al.getSequenceAt(i);
- }
- }
-
- return seqs;
- }
-}
+/*
+ * 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.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.schemes.*;
+
+/**
+ * Collects a set contiguous ranges on a set of sequences
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceGroup
+{
+ String groupName;
+
+ String description;
+
+ Conservation conserve;
+
+ Vector aaFrequency;
+
+ boolean displayBoxes = true;
+
+ boolean displayText = true;
+
+ boolean colourText = false;
+
+ /**
+ * after Olivier's non-conserved only character display
+ */
+ boolean showNonconserved = false;
+
+ /**
+ * group members
+ */
+ private Vector sequences = new Vector();
+
+ /**
+ * representative sequence for this group (if any)
+ */
+ private SequenceI seqrep = null;
+
+ int width = -1;
+
+ /**
+ * Colourscheme applied to group if any
+ */
+ public ColourSchemeI cs;
+
+ int startRes = 0;
+
+ int endRes = 0;
+
+ public Color outlineColour = Color.black;
+
+ public Color idColour = null;
+
+ public int thresholdTextColour = 0;
+
+ public Color textColour = Color.black;
+
+ public Color textColour2 = Color.white;
+
+ /**
+ * consensus calculation property
+ */
+ private boolean ignoreGapsInConsensus = true;
+
+ /**
+ * consensus calculation property
+ */
+ private boolean showSequenceLogo = false;
+
+ /**
+ * @return the includeAllConsSymbols
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return showSequenceLogo;
+ }
+
+ /**
+ * Creates a new SequenceGroup object.
+ */
+ public SequenceGroup()
+ {
+ groupName = "JGroup:" + this.hashCode();
+ }
+
+ /**
+ * Creates a new SequenceGroup object.
+ *
+ * @param sequences
+ * @param groupName
+ * @param scheme
+ * @param displayBoxes
+ * @param displayText
+ * @param colourText
+ * @param start
+ * first column of group
+ * @param end
+ * last column of group
+ */
+ public SequenceGroup(Vector sequences, String groupName,
+ ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
+ boolean colourText, int start, int end)
+ {
+ this.sequences = sequences;
+ this.groupName = groupName;
+ this.displayBoxes = displayBoxes;
+ this.displayText = displayText;
+ this.colourText = colourText;
+ this.cs = scheme;
+ startRes = start;
+ endRes = end;
+ recalcConservation();
+ }
+
+ /**
+ * copy constructor
+ *
+ * @param seqsel
+ */
+ public SequenceGroup(SequenceGroup seqsel)
+ {
+ if (seqsel != null)
+ {
+ sequences = new Vector();
+ Enumeration sq = seqsel.sequences.elements();
+ while (sq.hasMoreElements())
+ {
+ sequences.addElement(sq.nextElement());
+ }
+ ;
+ if (seqsel.groupName != null)
+ {
+ groupName = new String(seqsel.groupName);
+ }
+ displayBoxes = seqsel.displayBoxes;
+ displayText = seqsel.displayText;
+ colourText = seqsel.colourText;
+ startRes = seqsel.startRes;
+ endRes = seqsel.endRes;
+ cs = seqsel.cs;
+ if (seqsel.description != null)
+ description = new String(seqsel.description);
+ hidecols = seqsel.hidecols;
+ hidereps = seqsel.hidereps;
+ idColour = seqsel.idColour;
+ outlineColour = seqsel.outlineColour;
+ seqrep = seqsel.seqrep;
+ textColour = seqsel.textColour;
+ textColour2 = seqsel.textColour2;
+ thresholdTextColour = seqsel.thresholdTextColour;
+ width = seqsel.width;
+ ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
+ if (seqsel.conserve != null)
+ {
+ recalcConservation(); // safer than
+ // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
+ }
+ }
+ }
+
+ public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
+ {
+ int iSize = sequences.size();
+ SequenceI[] seqs = new SequenceI[iSize];
+ SequenceI[] inorder = getSequencesInOrder(align);
+
+ for (int i = 0, ipos = 0; i < inorder.length; i++)
+ {
+ SequenceI seq = inorder[i];
+
+ seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
+ if (seqs[ipos] != null)
+ {
+ seqs[ipos].setDescription(seq.getDescription());
+ seqs[ipos].setDBRef(seq.getDBRef());
+ seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+ if (seq.getDatasetSequence() != null)
+ {
+ seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
+ }
+
+ if (seq.getAnnotation() != null)
+ {
+ AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
+ // Only copy annotation that is either a score or referenced by the
+ // alignment's annotation vector
+ for (int a = 0; a < seq.getAnnotation().length; a++)
+ {
+ AlignmentAnnotation tocopy = seq.getAnnotation()[a];
+ if (alann != null)
+ {
+ boolean found = false;
+ for (int pos = 0; pos < alann.length; pos++)
+ {
+ if (alann[pos] == tocopy)
+ {
+ found = true;
+ break;
+ }
+ }
+ if (!found)
+ continue;
+ }
+ AlignmentAnnotation newannot = new AlignmentAnnotation(
+ seq.getAnnotation()[a]);
+ newannot.restrict(startRes, endRes);
+ newannot.setSequenceRef(seqs[ipos]);
+ newannot.adjustForAlignment();
+ seqs[ipos].addAlignmentAnnotation(newannot);
+ }
+ }
+ ipos++;
+ }
+ else
+ {
+ iSize--;
+ }
+ }
+ if (iSize != inorder.length)
+ {
+ SequenceI[] nseqs = new SequenceI[iSize];
+ System.arraycopy(seqs, 0, nseqs, 0, iSize);
+ seqs = nseqs;
+ }
+ return seqs;
+
+ }
+
+ /**
+ * If sequence ends in gaps, the end residue can be correctly calculated here
+ *
+ * @param seq
+ * SequenceI
+ * @return int
+ */
+ public int findEndRes(SequenceI seq)
+ {
+ int eres = 0;
+ char ch;
+
+ for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
+ {
+ ch = seq.getCharAt(j);
+ if (!jalview.util.Comparison.isGap((ch)))
+ {
+ eres++;
+ }
+ }
+
+ if (eres > 0)
+ {
+ eres += seq.getStart() - 1;
+ }
+
+ return eres;
+ }
+
+ public Vector getSequences(Hashtable hiddenReps)
+ {
+ if (hiddenReps == null)
+ {
+ return sequences;
+ }
+ else
+ {
+ Vector allSequences = new Vector();
+ SequenceI seq, seq2;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ seq = (SequenceI) sequences.elementAt(i);
+ allSequences.addElement(seq);
+ if (hiddenReps.containsKey(seq))
+ {
+ SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
+ for (int h = 0; h < hsg.getSize(); h++)
+ {
+ seq2 = hsg.getSequenceAt(h);
+ if (seq2 != seq && !allSequences.contains(seq2))
+ {
+ allSequences.addElement(seq2);
+ }
+ }
+ }
+ }
+
+ return allSequences;
+ }
+ }
+
+ public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+ {
+ Vector tmp = getSequences(hiddenReps);
+ if (tmp == null)
+ {
+ return null;
+ }
+ SequenceI[] result = new SequenceI[tmp.size()];
+ for (int i = 0; i < result.length; i++)
+ {
+ result[i] = (SequenceI) tmp.elementAt(i);
+ }
+
+ return result;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean adjustForRemoveLeft(int col)
+ {
+ // return value is true if the group still exists
+ if (startRes >= col)
+ {
+ startRes = startRes - col;
+ }
+
+ if (endRes >= col)
+ {
+ endRes = endRes - col;
+
+ if (startRes > endRes)
+ {
+ startRes = 0;
+ }
+ }
+ else
+ {
+ // must delete this group!!
+ return false;
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param col
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean adjustForRemoveRight(int col)
+ {
+ if (startRes > col)
+ {
+ // delete this group
+ return false;
+ }
+
+ if (endRes >= col)
+ {
+ endRes = col;
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName()
+ {
+ return groupName;
+ }
+
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name
+ * DOCUMENT ME!
+ */
+ public void setName(String name)
+ {
+ groupName = name;
+ // TODO: URGENT: update dependent objects (annotation row)
+ }
+
+ public void setDescription(String desc)
+ {
+ description = desc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Conservation getConservation()
+ {
+ return conserve;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ */
+ public void setConservation(Conservation c)
+ {
+ conserve = c;
+ }
+
+ /**
+ * Add s to this sequence group. If aligment sequence is already contained in
+ * group, it will not be added again, but recalculation may happen if the flag
+ * is set.
+ *
+ * @param s
+ * alignment sequence to be added
+ * @param recalc
+ * true means Group's conservation should be recalculated
+ */
+ public void addSequence(SequenceI s, boolean recalc)
+ {
+ if (s != null && !sequences.contains(s))
+ {
+ sequences.addElement(s);
+ }
+
+ if (recalc)
+ {
+ recalcConservation();
+ }
+ }
+
+ /**
+ * Max Gaps Threshold for performing a conservation calculation TODO: make
+ * this a configurable property - or global to an alignment view
+ */
+ private int consPercGaps = 25;
+
+ /**
+ * calculate residue conservation for group - but only if necessary.
+ */
+ public void recalcConservation()
+ {
+ if (cs == null && consensus == null && conservation == null)
+ {
+ return;
+ }
+
+ try
+ {
+ Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+ endRes + 1, showSequenceLogo);
+ if (consensus != null)
+ {
+ _updateConsensusRow(cnsns);
+ }
+ if (cs != null)
+ {
+ cs.setConsensus(cnsns);
+
+ if (cs instanceof ClustalxColourScheme)
+ {
+ ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+ }
+ }
+
+ if ((conservation != null)
+ || (cs != null && cs.conservationApplied()))
+ {
+ Conservation c = new Conservation(groupName,
+ ResidueProperties.propHash, 3, sequences, startRes,
+ endRes + 1);
+ c.calculate();
+ c.verdict(false, consPercGaps);
+ if (conservation != null)
+ {
+ _updateConservationRow(c);
+ }
+ if (cs != null)
+ {
+ if (cs.conservationApplied())
+ {
+ cs.setConservation(c);
+
+ if (cs instanceof ClustalxColourScheme)
+ {
+ ((ClustalxColourScheme) cs).resetClustalX(sequences,
+ getWidth());
+ }
+ }
+ }
+ }
+ } catch (java.lang.OutOfMemoryError err)
+ {
+ // TODO: catch OOM
+ System.out.println("Out of memory loading groups: " + err);
+ }
+
+ }
+
+ private void _updateConservationRow(Conservation c)
+ {
+ if (conservation == null)
+ {
+ getConservation();
+ }
+ // update Labels
+ conservation.label = "Conservation for " + getName();
+ conservation.description = "Conservation for group " + getName()
+ + " less than " + consPercGaps + "% gaps";
+ // preserve width if already set
+ int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
+ : endRes + 1)
+ : endRes + 1;
+ conservation.annotations = null;
+ conservation.annotations = new Annotation[aWidth]; // should be alignment
+ // width
+ c.completeAnnotations(conservation, null, startRes, endRes + 1);
+ }
+
+ public Hashtable[] consensusData = null;
+
+ private void _updateConsensusRow(Hashtable[] cnsns)
+ {
+ if (consensus == null)
+ {
+ getConsensus();
+ }
+ consensus.label = "Consensus for " + getName();
+ consensus.description = "Percent Identity";
+ consensusData = cnsns;
+ // preserve width if already set
+ int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
+ : endRes + 1)
+ : endRes + 1;
+ consensus.annotations = null;
+ consensus.annotations = new Annotation[aWidth]; // should be alignment width
+
+ AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
+ ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
+ // for
+ // ignoreGapsInConsensusCalculation);
+ }
+
+ /**
+ * @param s
+ * sequence to either add or remove from group
+ * @param recalc
+ * flag passed to delete/addSequence to indicate if group properties
+ * should be recalculated
+ */
+ public void addOrRemove(SequenceI s, boolean recalc)
+ {
+ if (sequences.contains(s))
+ {
+ deleteSequence(s, recalc);
+ }
+ else
+ {
+ addSequence(s, recalc);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ * @param recalc
+ * DOCUMENT ME!
+ */
+ public void deleteSequence(SequenceI s, boolean recalc)
+ {
+ sequences.removeElement(s);
+
+ if (recalc)
+ {
+ recalcConservation();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ /**
+ * Set the first column selected by this group. Runs from 0<=i 0)
+ {
+ width = ((SequenceI) sequences.elementAt(0)).getLength();
+ }
+
+ for (int i = 1; i < sequences.size(); i++)
+ {
+ SequenceI seq = (SequenceI) sequences.elementAt(i);
+
+ if (seq.getLength() > width)
+ {
+ width = seq.getLength();
+ }
+ }
+
+ return width;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ */
+ public void setOutlineColour(Color c)
+ {
+ outlineColour = c;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getOutlineColour()
+ {
+ return outlineColour;
+ }
+
+ /**
+ *
+ * returns the sequences in the group ordered by the ordering given by al.
+ * this used to return an array with null entries regardless, new behaviour is
+ * below. TODO: verify that this does not affect use in applet or application
+ *
+ * @param al
+ * Alignment
+ * @return SequenceI[] intersection of sequences in group with al, ordered by
+ * al, or null if group does not intersect with al
+ */
+ public SequenceI[] getSequencesInOrder(AlignmentI al)
+ {
+ return getSequencesInOrder(al, true);
+ }
+
+ /**
+ * return an array representing the intersection of the group with al,
+ * optionally returning an array the size of al.getHeight() where nulls mark
+ * the non-intersected sequences
+ *
+ * @param al
+ * @param trim
+ * @return null or array
+ */
+ public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
+ {
+ int sSize = sequences.size();
+ int alHeight = al.getHeight();
+
+ SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
+
+ int index = 0;
+ for (int i = 0; i < alHeight && index < sSize; i++)
+ {
+ if (sequences.contains(al.getSequenceAt(i)))
+ {
+ seqs[(trim) ? index : i] = al.getSequenceAt(i);
+ index++;
+ }
+ }
+ if (index == 0)
+ {
+ return null;
+ }
+ if (!trim)
+ {
+ return seqs;
+ }
+ if (index < seqs.length)
+ {
+ SequenceI[] dummy = seqs;
+ seqs = new SequenceI[index];
+ while (--index >= 0)
+ {
+ seqs[index] = dummy[index];
+ dummy[index] = null;
+ }
+ }
+ return seqs;
+ }
+
+ /**
+ * @return the idColour
+ */
+ public Color getIdColour()
+ {
+ return idColour;
+ }
+
+ /**
+ * @param idColour
+ * the idColour to set
+ */
+ public void setIdColour(Color idColour)
+ {
+ this.idColour = idColour;
+ }
+
+ /**
+ * @return the representative sequence for this group
+ */
+ public SequenceI getSeqrep()
+ {
+ return seqrep;
+ }
+
+ /**
+ * set the representative sequence for this group. Note - this affects the
+ * interpretation of the Hidereps attribute.
+ *
+ * @param seqrep
+ * the seqrep to set (null means no sequence representative)
+ */
+ public void setSeqrep(SequenceI seqrep)
+ {
+ this.seqrep = seqrep;
+ }
+
+ /**
+ *
+ * @return true if group has a sequence representative
+ */
+ public boolean hasSeqrep()
+ {
+ return seqrep != null;
+ }
+
+ /**
+ * visibility of rows or represented rows covered by group
+ */
+ private boolean hidereps = false;
+
+ /**
+ * set visibility of sequences covered by (if no sequence representative is
+ * defined) or represented by this group.
+ *
+ * @param visibility
+ */
+ public void setHidereps(boolean visibility)
+ {
+ hidereps = visibility;
+ }
+
+ /**
+ *
+ * @return true if sequences represented (or covered) by this group should be
+ * hidden
+ */
+ public boolean isHidereps()
+ {
+ return hidereps;
+ }
+
+ /**
+ * visibility of columns intersecting this group
+ */
+ private boolean hidecols = false;
+
+ /**
+ * set intended visibility of columns covered by this group
+ *
+ * @param visibility
+ */
+ public void setHideCols(boolean visibility)
+ {
+ hidecols = visibility;
+ }
+
+ /**
+ *
+ * @return true if columns covered by group should be hidden
+ */
+ public boolean isHideCols()
+ {
+ return hidecols;
+ }
+
+ /**
+ * create a new sequence group from the intersection of this group with an
+ * alignment Hashtable of hidden representatives
+ *
+ * @param alignment
+ * (may not be null)
+ * @param hashtable
+ * (may be null)
+ * @return new group containing sequences common to this group and alignment
+ */
+ public SequenceGroup intersect(AlignmentI alignment, Hashtable hashtable)
+ {
+ SequenceGroup sgroup = new SequenceGroup(this);
+ SequenceI[] insect = getSequencesInOrder(alignment);
+ sgroup.sequences = new Vector();
+ for (int s = 0; insect != null && s < insect.length; s++)
+ {
+ if (hashtable == null || hashtable.containsKey(insect[s]))
+ {
+ sgroup.sequences.addElement(insect[s]);
+ }
+ }
+ // Enumeration en =getSequences(hashtable).elements();
+ // while (en.hasMoreElements())
+ // {
+ // SequenceI elem = (SequenceI) en.nextElement();
+ // if (alignment.getSequences().contains(elem))
+ // {
+ // sgroup.addSequence(elem, false);
+ // }
+ // }
+ return sgroup;
+ }
+
+ /**
+ * @return the showUnconserved
+ */
+ public boolean getShowNonconserved()
+ {
+ return showNonconserved;
+ }
+
+ /**
+ * @param showNonconserved
+ * the showUnconserved to set
+ */
+ public void setShowNonconserved(boolean displayNonconserved)
+ {
+ this.showNonconserved = displayNonconserved;
+ }
+
+ AlignmentAnnotation consensus = null, conservation = null;
+
+ /**
+ * flag indicating if consensus histogram should be rendered
+ */
+ private boolean showConsensusHistogram;
+
+ /**
+ * set this alignmentAnnotation object as the one used to render consensus
+ * annotation
+ *
+ * @param aan
+ */
+ public void setConsensus(AlignmentAnnotation aan)
+ {
+ if (consensus == null)
+ {
+ consensus = aan;
+ }
+ }
+
+ /**
+ *
+ * @return automatically calculated consensus row
+ */
+ public AlignmentAnnotation getConsensus()
+ {
+ // TODO get or calculate and get consensus annotation row for this group
+ int aWidth = this.getWidth();
+ // pointer
+ // possibility
+ // here.
+ if (aWidth < 0)
+ {
+ return null;
+ }
+ if (consensus == null)
+ {
+ consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+ 100f, AlignmentAnnotation.BAR_GRAPH);
+ }
+ consensus.hasText = true;
+ consensus.autoCalculated = true;
+ consensus.groupRef = this;
+ consensus.label = "Consensus for " + getName();
+ consensus.description = "Percent Identity";
+ return consensus;
+ }
+
+ /**
+ * set this alignmentAnnotation object as the one used to render consensus
+ * annotation
+ *
+ * @param aan
+ */
+ public void setConservationRow(AlignmentAnnotation aan)
+ {
+ if (conservation == null)
+ {
+ conservation = aan;
+ }
+ }
+
+ /**
+ * get the conservation annotation row for this group
+ *
+ * @return autoCalculated annotation row
+ */
+ public AlignmentAnnotation getConservationRow()
+ {
+ if (conservation == null)
+ {
+ conservation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+ 11f, AlignmentAnnotation.BAR_GRAPH);
+ }
+
+ conservation.hasText = true;
+ conservation.autoCalculated = true;
+ conservation.groupRef = this;
+ conservation.label = "Conservation for " + getName();
+ conservation.description = "Conservation for group " + getName()
+ + " less than " + consPercGaps + "% gaps";
+ return conservation;
+ }
+
+ /**
+ *
+ * @return true if annotation rows have been instantiated for this group
+ */
+ public boolean hasAnnotationRows()
+ {
+ return consensus != null || conservation != null;
+ }
+
+ public SequenceI getConsensusSeq()
+ {
+ getConsensus();
+ StringBuffer seqs = new StringBuffer();
+ for (int i = 0; i < consensus.annotations.length; i++)
+ {
+ if (consensus.annotations[i] != null)
+ {
+ if (consensus.annotations[i].description.charAt(0) == '[')
+ {
+ seqs.append(consensus.annotations[i].description.charAt(1));
+ }
+ else
+ {
+ seqs.append(consensus.annotations[i].displayCharacter);
+ }
+ }
+ }
+
+ SequenceI sq = new Sequence("Group" + getName() + " Consensus",
+ seqs.toString());
+ sq.setDescription("Percentage Identity Consensus "
+ + ((ignoreGapsInConsensus) ? " without gaps" : ""));
+ return sq;
+ }
+
+ public void setIgnoreGapsConsensus(boolean state)
+ {
+ if (this.ignoreGapsInConsensus != state && consensus != null)
+ {
+ ignoreGapsInConsensus = state;
+ recalcConservation();
+ }
+ ignoreGapsInConsensus = state;
+ }
+
+ public boolean getIgnoreGapsConsensus()
+ {
+ return ignoreGapsInConsensus;
+ }
+
+ /**
+ * @param showSequenceLogo
+ * indicates if a sequence logo is shown for consensus annotation
+ */
+ public void setshowSequenceLogo(boolean showSequenceLogo)
+ {
+ // TODO: decouple calculation from settings update
+ if (this.showSequenceLogo != showSequenceLogo && consensus != null)
+ {
+ this.showSequenceLogo = showSequenceLogo;
+ recalcConservation();
+ }
+ this.showSequenceLogo = showSequenceLogo;
+ }
+
+ /**
+ *
+ * @param showConsHist
+ * flag indicating if the consensus histogram for this group should
+ * be rendered
+ */
+ public void setShowConsensusHistogram(boolean showConsHist)
+ {
+
+ if (showConsensusHistogram != showConsHist && consensus != null)
+ {
+ this.showConsensusHistogram = showConsHist;
+ recalcConservation();
+ }
+ this.showConsensusHistogram = showConsHist;
+ }
+
+ /**
+ * @return the showConsensusHistogram
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return showConsensusHistogram;
+ }
+}