-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.Vector;\r
-\r
-public class SequenceGroup\r
-{\r
- String groupName;\r
- Conservation conserve;\r
- Vector aaFrequency;\r
- boolean displayBoxes;\r
- boolean displayText;\r
- boolean colourText;\r
- public Vector sequences = new Vector();\r
- int width = -1;\r
- public ColourSchemeI cs;\r
- int startRes = 0;\r
- int endRes = 0;\r
- Color outlineColour = Color.black;\r
-\r
- public SequenceGroup()\r
- {\r
- groupName = "Group";\r
- this.displayBoxes = true;\r
- this.displayText = true;\r
- this.colourText = false;\r
- cs = null;\r
- }\r
-\r
- public SequenceGroup(Vector sequences, String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText,\r
- int start, int end)\r
- {\r
- this.sequences = sequences;\r
- this.groupName = groupName;\r
- this.displayBoxes = displayBoxes;\r
- this.displayText = displayText;\r
- this.colourText = colourText;\r
- this.cs = scheme;\r
- startRes = start;\r
- endRes = end;\r
- recalcConservation();\r
- }\r
-\r
- public SequenceGroup(String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText,\r
- int start, int end)\r
- {\r
- this.groupName = groupName;\r
- this.displayBoxes = displayBoxes;\r
- this.displayText = displayText;\r
- this.colourText = colourText;\r
- this.cs = scheme;\r
- startRes = start;\r
- endRes = end;\r
- }\r
-\r
- public boolean adjustForRemoveLeft(int col)\r
- {\r
- // return value is true if the group still exists\r
- if (startRes >= col)\r
- {\r
- startRes = startRes - col;\r
- }\r
-\r
- if (endRes >= col)\r
- {\r
- endRes = endRes - col;\r
-\r
- if (startRes > endRes)\r
- {\r
- startRes = 0;\r
- }\r
- }\r
- else\r
- {\r
- // must delete this group!!\r
- return false;\r
- }\r
-\r
- return true;\r
- }\r
-\r
- public boolean adjustForRemoveRight(int col)\r
- {\r
- if (startRes > col)\r
- {\r
- // delete this group\r
- return false;\r
- }\r
-\r
- if (endRes >= col)\r
- {\r
- endRes = col;\r
- }\r
-\r
- return true;\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, boolean recalc)\r
- {\r
- if (!sequences.contains(s))\r
- sequences.addElement(s);\r
-\r
- if(recalc)\r
- recalcConservation();\r
- }\r
-\r
-\r
- public void recalcConservation()\r
- {\r
- if (cs != null)\r
- {\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
- }\r
-\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) cs).resetClustalX(sequences,getWidth());\r
- }\r
-\r
-\r
- if ( cs instanceof ConservationColourScheme)\r
- {\r
- Conservation c = new Conservation(groupName,\r
- ResidueProperties.propHash, 3, sequences,\r
- 0, getWidth());\r
- c.calculate();\r
- c.verdict(false, 25);\r
-\r
- ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
- ccs.conserve = c;\r
- if (ccs.cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) ccs.cs).resetClustalX(sequences, getWidth());\r
- }\r
-\r
- }\r
- }\r
-\r
- public void addOrRemove(SequenceI s, boolean recalc)\r
- {\r
- if (sequences.contains(s))\r
- {\r
- deleteSequence(s, recalc);\r
- }\r
- else\r
- {\r
- addSequence(s, recalc);\r
- }\r
- }\r
-\r
- public void deleteSequence(SequenceI s, boolean recalc)\r
- {\r
- sequences.removeElement(s);\r
- if(recalc)\r
- recalcConservation();\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 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 getWidth()\r
- {\r
- // MC This needs to get reset when characters are inserted and deleted\r
- if (sequences.size() > 0)\r
- {\r
- width = ( (SequenceI) sequences.elementAt(0)).getLength();\r
- }\r
-\r
- for (int i = 1; i < sequences.size(); i++)\r
- {\r
- SequenceI seq = (SequenceI) sequences.elementAt(i);\r
-\r
- if (seq.getLength() > width)\r
- {\r
- width = seq.getLength();\r
- }\r
- }\r
-\r
- return width;\r
- }\r
-\r
- public void setOutlineColour(Color c)\r
- {\r
- outlineColour = c;\r
- }\r
-\r
- public Color getOutlineColour()\r
- {\r
- return outlineColour;\r
- }\r
-\r
- /**\r
- *\r
- * returns the sequences in the group ordered by the ordering given by al\r
- *\r
- * @param al Alignment\r
- * @return SequenceI[]\r
- */\r
- public SequenceI[] getSequencesInOrder(Alignment al)\r
- {\r
- int sz;\r
- java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
- SequenceI[] seqs = new SequenceI[sz = sequences.size()];\r
-\r
- for (int i = 0; i < sz; i++)\r
- {\r
- SequenceI seq = (SequenceI) sequences.elementAt(i);\r
- int index = al.findIndex(seq);\r
- orderedSeqs.put(index + "", seq);\r
- }\r
-\r
- int index = 0;\r
-\r
- for (int i = 0; i < sz; i++)\r
- {\r
- SequenceI seq = null;\r
-\r
- while (seq == null)\r
- {\r
- if (orderedSeqs.containsKey(index + ""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
-\r
- break;\r
- }\r
- else\r
- {\r
- index++;\r
- }\r
- }\r
-\r
- seqs[index] = seq;\r
- }\r
-\r
- return seqs;\r
- }\r
-}\r
+/*
+ * 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.*;
+
+/**
+ * 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;
+ private Vector sequences = new Vector();
+ int width = -1;
+
+ /** DOCUMENT ME!! */
+ 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;
+
+ /**
+ * 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();
+ }
+
+ 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;
+ }
+
+ 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
+ *
+ * @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();
+ }
+ }
+
+ /**
+ * calculate residue conservation for group
+ */
+ 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;
+ }
+
+ /**
+ * @return the idColour
+ */
+ public Color getIdColour()
+ {
+ return idColour;
+ }
+
+ /**
+ * @param idColour the idColour to set
+ */
+ public void setIdColour(Color idColour)
+ {
+ this.idColour = idColour;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff