-package jalview.datamodel;\r
-\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import java.util.Vector;\r
-\r
-public class SequenceGroup\r
-{\r
- String groupName;\r
- boolean isSelected;\r
- boolean displayBoxes;\r
- boolean displayText;\r
- boolean colourText;\r
- boolean display;\r
- Conservation conserve;\r
- Vector aaFrequency;\r
- boolean aaFrequencyValid = false;\r
- public Vector sequences = new Vector();\r
- int width = -1;\r
- public ColourSchemeI cs;\r
- int startRes = 0;\r
- int endRes = 0;\r
-\r
- public SequenceGroup()\r
- {\r
- groupName = "Group";\r
- this.isSelected = false;\r
- this.displayBoxes = true;\r
- this.displayText = true;\r
- this.colourText = false;\r
- this.display = true;\r
- cs = null;\r
- }\r
-\r
- public SequenceGroup(String groupName, ColourSchemeI scheme,\r
- boolean isSelected,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText,\r
- boolean display,\r
- int start,\r
- int end)\r
- {\r
-\r
- this.groupName = groupName;\r
- this.isSelected = isSelected;\r
- this.displayBoxes = displayBoxes;\r
- this.displayText = displayText;\r
- this.colourText = colourText;\r
- this.display = display;\r
- this.cs = scheme;\r
- startRes = start;\r
- endRes = end;\r
- }\r
-\r
- public String getName()\r
- {\r
- return groupName;\r
- }\r
-\r
- public void setName(String name)\r
- {\r
- groupName = name;\r
- }\r
-\r
- public Conservation getConservation()\r
- {\r
- return conserve;\r
- }\r
-\r
- public void setConservation(Conservation c)\r
- {\r
- conserve = c;\r
- }\r
-\r
- public void addSequence(SequenceI s)\r
- {\r
- if(!sequences.contains(s))\r
- sequences.addElement(s);\r
- }\r
-\r
- public void addOrRemove(SequenceI s)\r
- {\r
- if(sequences.contains(s))\r
- deleteSequence(s);\r
- else\r
- addSequence(s);\r
- }\r
-\r
- public void deleteSequence(SequenceI s)\r
- {\r
- sequences.removeElement(s);\r
- }\r
-\r
- public void setColourText(boolean state)\r
- {\r
- colourText = state;\r
- }\r
-\r
- public boolean getColourText()\r
- {\r
- return colourText;\r
- }\r
-\r
- public void setDisplayText(boolean state)\r
- {\r
- displayText = state;\r
- }\r
-\r
- public boolean getDisplayText()\r
- {\r
- return displayText;\r
- }\r
-\r
- public void setDisplayBoxes(boolean state)\r
- {\r
- displayBoxes = state;\r
- }\r
-\r
- public boolean getDisplayBoxes()\r
- {\r
- return displayBoxes;\r
- }\r
-\r
- public int getStartRes()\r
- {\r
- return startRes;\r
- }\r
-\r
- public int getEndRes()\r
- {\r
- return endRes;\r
- }\r
-\r
- public void setStartRes(int i)\r
- {\r
- startRes = i;\r
- }\r
-\r
- public void setEndRes(int i)\r
- {\r
- endRes = i;\r
- }\r
-\r
- public int getSize()\r
- {\r
- return sequences.size();\r
- }\r
-\r
- public SequenceI getSequenceAt(int i)\r
- {\r
- return (SequenceI) sequences.elementAt(i);\r
- }\r
-\r
- public Vector getAAFrequency()\r
- {\r
- if (aaFrequency == null || aaFrequencyValid == false)\r
- {\r
- aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());\r
- aaFrequencyValid = true;\r
- }\r
- return aaFrequency;\r
- }\r
-\r
- public int getWidth()\r
- {\r
- System.out.println("it is called");\r
- // MC This needs to get reset when characters are inserted and deleted\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- SequenceI seq = (SequenceI) sequences.elementAt(i);\r
- if (seq.getLength() > width)\r
- width = seq.getLength();\r
- }\r
- return width;\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+/**
+ * Collects a set contiguous ranges on a set of sequences
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceGroup implements AnnotatedCollectionI
+{
+ 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 List<SequenceI> sequences = new ArrayList<SequenceI>();
+
+ /**
+ * representative sequence for this group (if any)
+ */
+ private SequenceI seqrep = null;
+
+ int width = -1;
+
+ /**
+ * Colourscheme applied to group if any
+ */
+ public ColourSchemeI cs;
+
+ // start column (base 0)
+ int startRes = 0;
+
+ // end column (base 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;
+
+ /**
+ * flag indicating if logo should be rendered normalised
+ */
+ private boolean normaliseSequenceLogo;
+
+ /**
+ * @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(List<SequenceI> 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 ArrayList<SequenceI>();
+ sequences.addAll(seqsel.sequences);
+ 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;
+ }
+
+ @Override
+ public List<SequenceI> getSequences()
+ {
+ return sequences;
+ }
+
+ @Override
+ public List<SequenceI> getSequences(
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ if (hiddenReps == null)
+ {
+ // TODO: need a synchronizedCollection here ?
+ return sequences;
+ }
+ else
+ {
+ List<SequenceI> allSequences = new ArrayList<SequenceI>();
+ for (SequenceI seq : sequences)
+ {
+ allSequences.add(seq);
+ if (hiddenReps.containsKey(seq))
+ {
+ SequenceCollectionI hsg = hiddenReps.get(seq);
+ for (SequenceI seq2 : hsg.getSequences())
+ {
+ if (seq2 != seq && !allSequences.contains(seq2))
+ {
+ allSequences.add(seq2);
+ }
+ }
+ }
+ }
+
+ return allSequences;
+ }
+ }
+
+ public SequenceI[] getSequencesAsArray(
+ Map<SequenceI, SequenceCollectionI> map)
+ {
+ List<SequenceI> tmp = getSequences(map);
+ if (tmp == null)
+ {
+ return null;
+ }
+ return tmp.toArray(new SequenceI[tmp.size()]);
+ }
+
+ /**
+ * 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)
+ {
+ synchronized (sequences)
+ {
+ if (s != null && !sequences.contains(s))
+ {
+ sequences.add(s);
+ }
+
+ if (recalc)
+ {
+ recalcConservation();
+ }
+ }
+ }
+
+ /**
+ * Max Gaps Threshold (percent) for performing a conservation calculation
+ */
+ private int consPercGaps = 25;
+
+ /**
+ * @return Max Gaps Threshold for performing a conservation calculation
+ */
+ public int getConsPercGaps()
+ {
+ return consPercGaps;
+ }
+
+ /**
+ * set Max Gaps Threshold (percent) for performing a conservation calculation
+ *
+ * @param consPercGaps
+ */
+ public void setConsPercGaps(int consPercGaps)
+ {
+ this.consPercGaps = consPercGaps;
+ }
+
+ /**
+ * 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, sequences.size());
+ }
+ if (cs != null)
+ {
+ cs.setConsensus(cnsns);
+ }
+
+ 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 != null)
+ {
+ cs.alignmentChanged(context != null ? context : this, null);
+ }
+ } 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, long nseq)
+ {
+ 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, nseq); // 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)
+ {
+ synchronized (sequences)
+ {
+ if (sequences.contains(s))
+ {
+ deleteSequence(s, recalc);
+ }
+ else
+ {
+ addSequence(s, recalc);
+ }
+ }
+ }
+
+ /**
+ * remove
+ *
+ * @param s
+ * to be removed
+ * @param recalc
+ * true means recalculate conservation
+ */
+ public void deleteSequence(SequenceI s, boolean recalc)
+ {
+ synchronized (sequences)
+ {
+ sequences.remove(s);
+
+ if (recalc)
+ {
+ recalcConservation();
+ }
+ }
+ }
+
+ /**
+ *
+ *
+ * @return the first column selected by this group. Runs from 0<=i<N_cols
+ */
+ @Override
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ /**
+ *
+ * @return the groups last selected column. Runs from 0<=i<N_cols
+ */
+ @Override
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ /**
+ * Set the first column selected by this group. Runs from 0<=i<N_cols
+ *
+ * @param i
+ */
+ public void setStartRes(int i)
+ {
+ startRes = i;
+ }
+
+ /**
+ * Set the groups last selected column. Runs from 0<=i<N_cols
+ *
+ * @param i
+ */
+ public void setEndRes(int i)
+ {
+ endRes = i;
+ }
+
+ /**
+ * @return number of sequences in group
+ */
+ public int getSize()
+ {
+ return sequences.size();
+ }
+
+ /**
+ * @param i
+ * @return the ith sequence
+ */
+ public SequenceI getSequenceAt(int i)
+ {
+ return sequences.get(i);
+ }
+
+ /**
+ * @param state
+ * colourText
+ */
+ 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;
+ }
+
+ /**
+ * computes the width of current set of sequences and returns it
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getWidth()
+ {
+ synchronized (sequences)
+ {
+ // MC This needs to get reset when characters are inserted and deleted
+ boolean first = true;
+ for (SequenceI seq : sequences)
+ {
+ if (first || seq.getLength() > width)
+ {
+ width = seq.getLength();
+ first = false;
+ }
+ }
+ 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)
+ {
+ synchronized (sequences)
+ {
+ 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 map
+ * (may be null)
+ * @return new group containing sequences common to this group and alignment
+ */
+ public SequenceGroup intersect(AlignmentI alignment,
+ Map<SequenceI, SequenceCollectionI> map)
+ {
+ SequenceGroup sgroup = new SequenceGroup(this);
+ SequenceI[] insect = getSequencesInOrder(alignment);
+ sgroup.sequences = new ArrayList<SequenceI>();
+ for (int s = 0; insect != null && s < insect.length; s++)
+ {
+ if (map == null || map.containsKey(insect[s]))
+ {
+ sgroup.sequences.add(insect[s]);
+ }
+ }
+ 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;
+ }
+
+ /**
+ * set flag indicating if logo should be normalised when rendered
+ *
+ * @param norm
+ */
+ public void setNormaliseSequenceLogo(boolean norm)
+ {
+ normaliseSequenceLogo = norm;
+ }
+
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ @Override
+ /**
+ * returns a new array with all annotation involving this group
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation()
+ {
+ // TODO add in other methods like 'getAlignmentAnnotation(String label),
+ // etc'
+ ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
+ synchronized (sequences)
+ {
+ for (SequenceI seq : sequences)
+ {
+ AlignmentAnnotation[] aa = seq.getAnnotation();
+ if (aa != null)
+ {
+ for (AlignmentAnnotation al : aa)
+ {
+ if (al.groupRef == this)
+ {
+ annot.add(al);
+ }
+ }
+ }
+ }
+ if (consensus != null)
+ {
+ annot.add(consensus);
+ }
+ if (conservation != null)
+ {
+ annot.add(conservation);
+ }
+ }
+ return annot.toArray(new AlignmentAnnotation[0]);
+ }
+
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
+ {
+ if (a.getCalcId() == calcId)
+ {
+ aa.add(a);
+ }
+ }
+ return aa;
+ }
+
+ /**
+ * Returns a list of annotations that match the specified sequenceRef, calcId
+ * and label, ignoring null values.
+ *
+ * @return list of AlignmentAnnotation objects
+ */
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation ann : getAlignmentAnnotation())
+ {
+ if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+ && ann.sequenceRef != null && ann.sequenceRef == seq
+ && ann.label != null && ann.label.equals(label))
+ {
+ aa.add(ann);
+ }
+ }
+ return aa;
+ }
+
+ /**
+ * Answer true if any annotation matches the calcId passed in (if not null).
+ *
+ * @param calcId
+ * @return
+ */
+ public boolean hasAnnotation(String calcId)
+ {
+ if (calcId != null && !"".equals(calcId))
+ {
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
+ {
+ if (a.getCalcId() == calcId)
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Remove all sequences from the group (leaving other properties unchanged).
+ */
+ public void clear()
+ {
+ synchronized (sequences)
+ {
+ sequences.clear();
+ }
+ }
+
+ private AnnotatedCollectionI context;
+
+ /**
+ * set the alignment or group context for this group
+ *
+ * @param context
+ */
+ public void setContext(AnnotatedCollectionI context)
+ {
+ this.context = context;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return context;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff