-/*\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.util.*;\r
-\r
-import java.util.*;\r
-\r
-/** Data structure to hold and manipulate a multiple sequence alignment\r
- */\r
-public class Alignment implements AlignmentI\r
-{\r
- protected Alignment dataset;\r
- protected Vector sequences;\r
- protected Vector groups = new Vector();\r
- protected char gapCharacter = '-';\r
- protected int type = NUCLEOTIDE;\r
- public static final int PROTEIN = 0;\r
- public static final int NUCLEOTIDE = 1;\r
-\r
- /** DOCUMENT ME!! */\r
- public AlignmentAnnotation[] annotations;\r
-\r
- HiddenSequences hiddenSequences = new HiddenSequences(this);\r
-\r
-\r
- /** Make an alignment from an array of Sequences.\r
- *\r
- * @param sequences\r
- */\r
- public Alignment(SequenceI[] seqs)\r
- {\r
- int i=0;\r
-\r
- if( jalview.util.Comparison.isNucleotide(seqs))\r
- type = NUCLEOTIDE;\r
- else\r
- type = PROTEIN;\r
-\r
- sequences = new Vector();\r
-\r
- for (i = 0; i < seqs.length; i++)\r
- {\r
- sequences.addElement(seqs[i]);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getSequences()\r
- {\r
- return sequences;\r
- }\r
-\r
- public SequenceI [] getSequencesArray()\r
- {\r
- SequenceI [] reply = new SequenceI[sequences.size()];\r
- for(int i=0; i<sequences.size(); i++)\r
- {\r
- reply[i] = (SequenceI)sequences.elementAt(i);\r
- }\r
- return reply;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceI getSequenceAt(int i)\r
- {\r
- if (i < sequences.size())\r
- {\r
- return (SequenceI) sequences.elementAt(i);\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /** Adds a sequence to the alignment. Recalculates maxLength and size.\r
- *\r
- * @param snew\r
- */\r
- public void addSequence(SequenceI snew)\r
- {\r
- if(dataset!=null)\r
- {\r
- if(snew.getDatasetSequence()!=null)\r
- {\r
- System.out.println(snew.getName());\r
- getDataset().addSequence(snew.getDatasetSequence());\r
- }\r
- else\r
- {\r
- Sequence ds = new Sequence(snew.getName(),\r
- AlignSeq.extractGaps("-. ",\r
- snew.getSequence()),\r
- snew.getStart(),\r
- snew.getEnd());\r
-\r
- snew.setDatasetSequence(ds);\r
- getDataset().addSequence(ds);\r
- }\r
- }\r
-\r
- sequences.addElement(snew);\r
- }\r
-\r
-\r
- /** Adds a sequence to the alignment. Recalculates maxLength and size.\r
- *\r
- * @param snew\r
- */\r
- public void setSequenceAt(int i, SequenceI snew)\r
- {\r
- SequenceI oldseq = getSequenceAt(i);\r
- deleteSequence(oldseq);\r
-\r
- sequences.setElementAt(snew, i);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getGroups()\r
- {\r
- return groups;\r
- }\r
-\r
- /** Takes out columns consisting entirely of gaps (-,.," ")\r
- */\r
- public void removeGaps()\r
- {\r
- SequenceI[] seqs = getVisibleAndRepresentedSeqs();\r
- int j, jSize = seqs.length;\r
-\r
- int width = 0;\r
- for (int i = 0; i < jSize; i++)\r
- {\r
- if (seqs[i].getLength() > width)\r
- {\r
- width = seqs[i].getLength();\r
- }\r
- }\r
-\r
- int startCol = -1, endCol = -1;\r
- boolean delete = true;\r
- for (int i = 0; i < width; i++)\r
- {\r
- delete = true;\r
-\r
- for (j = 0; j < jSize; j++)\r
- {\r
- if (seqs[j].getLength() > i)\r
- {\r
- if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))\r
- {\r
- if(delete)\r
- endCol = i;\r
-\r
- delete = false;\r
- break;\r
- }\r
- }\r
-\r
- }\r
-\r
- if(delete && startCol==-1)\r
- {\r
- startCol = i;\r
- }\r
-\r
-\r
- if (!delete && startCol > -1)\r
- {\r
- deleteColumns(seqs, startCol, endCol);\r
- width -= (endCol - startCol);\r
- i -= (endCol - startCol);\r
- startCol = -1;\r
- endCol = -1;\r
- }\r
- }\r
-\r
- if (delete && startCol > -1)\r
- {\r
- deleteColumns(seqs, startCol, endCol);\r
- }\r
-\r
- }\r
-\r
- /** Removes a range of columns (start to end inclusive).\r
- *\r
- * @param seqs Sequences to remove columns from\r
- * @param start Start column in the alignment\r
- * @param end End column in the alignment\r
- */\r
- public void deleteColumns(SequenceI [] seqs, int start, int end)\r
- {\r
- for(int i=0; i<seqs.length; i++)\r
- seqs[i].deleteChars(start, end);\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- public void trimLeft(int i)\r
- {\r
- SequenceI[] seqs = getVisibleAndRepresentedSeqs();\r
- int j, jSize = seqs.length;\r
- for (j = 0; j < jSize; j++)\r
- {\r
- int newstart = seqs[j].findPosition(i);\r
-\r
- if(i>seqs[j].getLength())\r
- {\r
- sequences.removeElement(seqs[j]);\r
- j--;\r
- jSize--;\r
- }\r
- else\r
- {\r
- seqs[j].setStart(newstart);\r
- seqs[j].setSequence(seqs[j].getSequence().substring(i));\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- public void trimRight(int i)\r
- {\r
- SequenceI[] seqs = getVisibleAndRepresentedSeqs();\r
- int j, jSize = seqs.length;\r
- for (j = 0; j < jSize; j++)\r
- {\r
- int newend = seqs[j].findPosition(i);\r
-\r
- seqs[j].setEnd(newend);\r
- if(seqs[j].getLength()>i)\r
- seqs[j].setSequence(seqs[j].getSequence().substring(0, i + 1));\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- */\r
- public void deleteSequence(SequenceI s)\r
- {\r
- for (int i = 0; i < getHeight(); i++)\r
- {\r
- if (getSequenceAt(i) == s)\r
- {\r
- deleteSequence(i);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- public void deleteSequence(int i)\r
- {\r
- sequences.removeElementAt(i);\r
- }\r
-\r
-\r
- /** */\r
- public SequenceGroup findGroup(SequenceI s)\r
- {\r
- for (int i = 0; i < this.groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
- if (sg.getSequences(false).contains(s))\r
- {\r
- return sg;\r
- }\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceGroup[] findAllGroups(SequenceI s)\r
- {\r
- Vector temp = new Vector();\r
-\r
- int gSize = groups.size();\r
- for (int i = 0; i < gSize; i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if(sg==null || sg.getSequences(false)==null)\r
- {\r
- this.deleteGroup(sg);\r
- gSize--;\r
- continue;\r
- }\r
-\r
- if (sg.getSequences(false).contains(s))\r
- {\r
- temp.addElement(sg);\r
- }\r
- }\r
-\r
- SequenceGroup[] ret = new SequenceGroup[temp.size()];\r
-\r
- for (int i = 0; i < temp.size(); i++)\r
- {\r
- ret[i] = (SequenceGroup) temp.elementAt(i);\r
- }\r
-\r
- return ret;\r
- }\r
-\r
-\r
-\r
- /** */\r
- public void addGroup(SequenceGroup sg)\r
- {\r
- if (!groups.contains(sg))\r
- {\r
- groups.addElement(sg);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void deleteAllGroups()\r
- {\r
- groups.removeAllElements();\r
-\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- SequenceI s = getSequenceAt(i);\r
- s.setColor(java.awt.Color.white);\r
- i++;\r
- }\r
- }\r
-\r
- /** */\r
- public void deleteGroup(SequenceGroup g)\r
- {\r
- if (groups.contains(g))\r
- {\r
- groups.removeElement(g);\r
- }\r
- }\r
-\r
- /** */\r
- public SequenceI findName(String name)\r
- {\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- if (getSequenceAt(i).getName().equals(name))\r
- {\r
- return getSequenceAt(i);\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return null;\r
- }\r
-\r
-\r
- /** */\r
- public int findIndex(SequenceI s)\r
- {\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- if (s == getSequenceAt(i))\r
- {\r
- return i;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return -1;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getHeight()\r
- {\r
- return sequences.size();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getWidth()\r
- {\r
- int maxLength = -1;\r
-\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- if (getSequenceAt(i).getLength() > maxLength)\r
- {\r
- maxLength = getSequenceAt(i).getLength();\r
- }\r
- }\r
-\r
- return maxLength;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getMaxIdLength()\r
- {\r
- int max = 0;\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- SequenceI seq = getSequenceAt(i);\r
- String tmp = seq.getName() + "/" + seq.getStart() + "-" +\r
- seq.getEnd();\r
-\r
- if (tmp.length() > max)\r
- {\r
- max = tmp.length();\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return max;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param gc DOCUMENT ME!\r
- */\r
- public void setGapCharacter(char gc)\r
- {\r
- gapCharacter = gc;\r
-\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- Sequence seq = (Sequence) sequences.elementAt(i);\r
- seq.setSequence( seq.getSequence().replace('.', gc) );\r
- seq.setSequence( seq.getSequence().replace('-', gc) );\r
- seq.setSequence( seq.getSequence().replace(' ', gc) );\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public char getGapCharacter()\r
- {\r
- return gapCharacter;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getAAFrequency()\r
- {\r
- return AAFrequency.calculate(sequences, 0, getWidth());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean isAligned()\r
- {\r
- int width = getWidth();\r
-\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- if (getSequenceAt(i).getLength() != width)\r
- {\r
- return false;\r
- }\r
- }\r
-\r
- return true;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param aa DOCUMENT ME!\r
- */\r
- public void deleteAnnotation(AlignmentAnnotation aa)\r
- {\r
- int aSize = 1;\r
-\r
- if (annotations != null)\r
- {\r
- aSize = annotations.length;\r
- }\r
-\r
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];\r
-\r
- int tIndex = 0;\r
-\r
- for (int i = 0; i < aSize; i++)\r
- {\r
- if (annotations[i] == aa)\r
- {\r
- continue;\r
- }\r
-\r
- temp[tIndex] = annotations[i];\r
- tIndex++;\r
- }\r
-\r
- annotations = temp;\r
- }\r
-\r
-\r
- public void adjustSequenceAnnotations()\r
- {\r
- if(annotations!=null)\r
- {\r
- for (int a = 0; a < annotations.length; a++)\r
- {\r
- if (annotations[a].sequenceRef != null)\r
- {\r
- annotations[a].adjustForAlignment();\r
- }\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param aa DOCUMENT ME!\r
- */\r
- public void addAnnotation(AlignmentAnnotation aa)\r
- {\r
- int aSize = 1;\r
- if (annotations != null)\r
- {\r
- aSize = annotations.length + 1;\r
- }\r
-\r
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
-\r
- temp[aSize-1] = aa;\r
-\r
- int i = 0;\r
-\r
- if (aSize > 1)\r
- {\r
- for (i = 0; i < (aSize-1); i++)\r
- {\r
- temp[i] = annotations[i];\r
- }\r
- }\r
-\r
- annotations = temp;\r
- }\r
-\r
- public void setAnnotationIndex(AlignmentAnnotation aa, int index)\r
- {\r
- if(aa==null || annotations==null || annotations.length-1<index)\r
- return;\r
-\r
- int aSize = annotations.length;\r
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
-\r
- temp[index] = aa;\r
-\r
- for (int i = 0; i < aSize; i++)\r
- {\r
- if(i==index)\r
- continue;\r
-\r
- if(i<index)\r
- temp[i] = annotations[i];\r
- else\r
- temp[i] = annotations[i-1];\r
- }\r
-\r
- annotations = temp;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public AlignmentAnnotation[] getAlignmentAnnotation()\r
- {\r
- return annotations;\r
- }\r
-\r
- public void setNucleotide(boolean b)\r
- {\r
- if(b)\r
- type = NUCLEOTIDE;\r
- else\r
- type = PROTEIN;\r
- }\r
-\r
- public boolean isNucleotide()\r
- {\r
- if(type==NUCLEOTIDE)\r
- return true;\r
- else\r
- return false;\r
- }\r
-\r
- public void setDataset(Alignment data)\r
- {\r
- if(dataset==null && data==null)\r
- {\r
- // Create a new dataset for this alignment.\r
- // Can only be done once, if dataset is not null\r
- // This will not be performed\r
- Sequence[] seqs = new Sequence[getHeight()];\r
- for (int i = 0; i < getHeight(); i++)\r
- {\r
- if(getSequenceAt(i).getDatasetSequence()!=null)\r
- {\r
- seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence();\r
- }\r
- else\r
- {\r
- seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
- AlignSeq.extractGaps(\r
- jalview.util.Comparison.GapChars,\r
- getSequenceAt(i).getSequence()\r
- ),\r
- getSequenceAt(i).getStart(),\r
- getSequenceAt(i).getEnd());\r
-\r
- getSequenceAt(i).setDatasetSequence(seqs[i]);\r
- }\r
- }\r
-\r
- dataset = new Alignment(seqs);\r
- }\r
- else if(dataset==null && data!=null)\r
- {\r
- dataset = data;\r
- }\r
- }\r
-\r
- public Alignment getDataset()\r
- {\r
- return dataset;\r
- }\r
-\r
- public boolean padGaps() {\r
- boolean modified=false;\r
-\r
- //Remove excess gaps from the end of alignment\r
- int maxLength = -1;\r
-\r
- SequenceI current;\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- current = getSequenceAt(i);\r
- for (int j = current.getLength(); j > maxLength; j--)\r
- {\r
- if (j > maxLength && !jalview.util.Comparison.isGap(\r
- current.getCharAt(j)))\r
- {\r
- maxLength = j;\r
- break;\r
- }\r
- }\r
- }\r
-\r
- maxLength++;\r
-\r
- for (int i = 0; i < sequences.size();\r
- i++)\r
- {\r
- current = getSequenceAt(i);\r
-\r
- if (current.getLength() < maxLength)\r
- {\r
- current.insertCharAt(maxLength - 1, gapCharacter);\r
- modified=true;\r
- }\r
- else if(current.getLength() > maxLength)\r
- {\r
- current.deleteChars(maxLength, current.getLength());\r
- }\r
- }\r
- return modified;\r
- }\r
-\r
- public HiddenSequences getHiddenSequences()\r
- {\r
- return hiddenSequences;\r
- }\r
-\r
- SequenceI [] getVisibleAndRepresentedSeqs()\r
- {\r
- if(hiddenSequences==null || hiddenSequences.getSize()<1)\r
- return getSequencesArray();\r
-\r
- Vector seqs = new Vector();\r
- SequenceI seq;\r
- SequenceGroup hidden;\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- seq = (SequenceI) sequences.elementAt(i);\r
- seqs.addElement(seq);\r
- hidden = seq.getHiddenSequences();\r
- if(hidden!=null)\r
- {\r
- for(int j=0; j<hidden.getSize(false); j++)\r
- {\r
- seqs.addElement(hidden.getSequenceAt(j));\r
- }\r
- }\r
- }\r
- SequenceI [] result = new SequenceI[seqs.size()];\r
- for(int i=0; i<seqs.size(); i++)\r
- result[i] = (SequenceI)seqs.elementAt(i);\r
-\r
- return result;\r
-\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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 jalview.analysis.*;
+
+import jalview.util.*;
+
+import java.util.*;
+
+/** Data structure to hold and manipulate a multiple sequence alignment
+ */
+public class Alignment implements AlignmentI
+{
+ protected Alignment dataset;
+ protected Vector sequences;
+ protected Vector groups = new Vector();
+ protected char gapCharacter = '-';
+ protected int type = NUCLEOTIDE;
+ public static final int PROTEIN = 0;
+ public static final int NUCLEOTIDE = 1;
+
+ /** DOCUMENT ME!! */
+ public AlignmentAnnotation[] annotations;
+
+ HiddenSequences hiddenSequences = new HiddenSequences(this);
+
+ private void initAlignment(SequenceI[] seqs) {
+ int i=0;
+
+ if( jalview.util.Comparison.isNucleotide(seqs))
+ type = NUCLEOTIDE;
+ else
+ type = PROTEIN;
+
+ sequences = new Vector();
+
+ for (i = 0; i < seqs.length; i++)
+ {
+ sequences.addElement(seqs[i]);
+ }
+
+ }
+ /** Make an alignment from an array of Sequences.
+ *
+ * @param sequences
+ */
+ public Alignment(SequenceI[] seqs)
+ {
+ initAlignment(seqs);
+ }
+ /**
+ * Make a new alignment from an array of SeqCigars
+ * @param seqs SeqCigar[]
+ */
+ public Alignment(SeqCigar[] alseqs) {
+
+ SequenceI[] seqs = new SequenceI[alseqs.length];
+ for (int i=0; i<alseqs.length; i++) {
+ seqs[i] = alseqs[i].getSeq(this.gapCharacter);
+ }
+ initAlignment(seqs);
+ }
+ /**
+ * Make a new alignment from an CigarArray
+ * JBPNote - can only do this when compactAlignment does not contain hidden regions.
+ * JBPNote - must also check that compactAlignment resolves to a set of SeqCigars - or construct them appropriately.
+ * @param compactAlignment CigarArray
+ */
+ public Alignment(CigarArray compactAlignment) {
+ throw new Error("Alignment(CigarArray) not yet implemented");
+ // this(compactAlignment.refCigars);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getSequences()
+ {
+ return sequences;
+ }
+
+ public SequenceI [] getSequencesArray()
+ {
+ SequenceI [] reply = new SequenceI[sequences.size()];
+ for(int i=0; i<sequences.size(); i++)
+ {
+ reply[i] = (SequenceI)sequences.elementAt(i);
+ }
+ return reply;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceI getSequenceAt(int i)
+ {
+ if (i < sequences.size())
+ {
+ return (SequenceI) sequences.elementAt(i);
+ }
+
+ return null;
+ }
+
+ /** Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
+ * @param snew
+ */
+ public void addSequence(SequenceI snew)
+ {
+ if(dataset!=null)
+ {
+ if(snew.getDatasetSequence()!=null)
+ {
+ System.out.println(snew.getName());
+ getDataset().addSequence(snew.getDatasetSequence());
+ }
+ else
+ {
+ Sequence ds = new Sequence(snew.getName(),
+ AlignSeq.extractGaps("-. ",
+ snew.getSequence()),
+ snew.getStart(),
+ snew.getEnd());
+
+ snew.setDatasetSequence(ds);
+ getDataset().addSequence(ds);
+ }
+ }
+
+ sequences.addElement(snew);
+ }
+
+
+ /** Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
+ * @param snew
+ */
+ public void setSequenceAt(int i, SequenceI snew)
+ {
+ SequenceI oldseq = getSequenceAt(i);
+ deleteSequence(oldseq);
+
+ sequences.setElementAt(snew, i);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getGroups()
+ {
+ return groups;
+ }
+
+ /** Takes out columns consisting entirely of gaps (-,.," ")
+ */
+ public void removeGaps()
+ {
+ SequenceI[] seqs = getVisibleAndRepresentedSeqs();
+ int j, jSize = seqs.length;
+
+ int width = 0;
+ for (int i = 0; i < jSize; i++)
+ {
+ if (seqs[i].getLength() > width)
+ {
+ width = seqs[i].getLength();
+ }
+ }
+
+ int startCol = -1, endCol = -1;
+ boolean delete = true;
+ for (int i = 0; i < width; i++)
+ {
+ delete = true;
+
+ for (j = 0; j < jSize; j++)
+ {
+ if (seqs[j].getLength() > i)
+ {
+ if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
+ {
+ if(delete)
+ endCol = i;
+
+ delete = false;
+ break;
+ }
+ }
+ }
+
+ if(delete && startCol==-1)
+ {
+ startCol = i;
+ }
+
+
+ if (!delete && startCol > -1)
+ {
+ deleteColumns(seqs, startCol, endCol);
+ width -= (endCol - startCol);
+ i -= (endCol - startCol);
+ startCol = -1;
+ endCol = -1;
+ }
+ }
+
+ if (delete && startCol > -1)
+ {
+ deleteColumns(seqs, startCol, endCol);
+ }
+ }
+
+ /** Removes a range of columns (start to end inclusive).
+ *
+ * @param seqs Sequences to remove columns from
+ * @param start Start column in the alignment
+ * @param end End column in the alignment
+ */
+ public void deleteColumns(SequenceI [] seqs, int start, int end)
+ {
+ for(int i=0; i<seqs.length; i++)
+ seqs[i].deleteChars(start, end);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ */
+ public void trimLeft(int i)
+ {
+ SequenceI[] seqs = getVisibleAndRepresentedSeqs();
+ int j, jSize = seqs.length;
+ for (j = 0; j < jSize; j++)
+ {
+ int newstart = seqs[j].findPosition(i);
+
+ if(i>seqs[j].getLength())
+ {
+ sequences.removeElement(seqs[j]);
+ j--;
+ jSize--;
+ }
+ else
+ {
+ seqs[j].setStart(newstart);
+ seqs[j].setSequence(seqs[j].getSequence().substring(i));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ */
+ public void trimRight(int i)
+ {
+ SequenceI[] seqs = getVisibleAndRepresentedSeqs();
+ int j, jSize = seqs.length;
+ for (j = 0; j < jSize; j++)
+ {
+ int newend = seqs[j].findPosition(i);
+
+ seqs[j].setEnd(newend);
+ if(seqs[j].getLength()>i)
+ seqs[j].setSequence(seqs[j].getSequence().substring(0, i + 1));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ */
+ public void deleteSequence(SequenceI s)
+ {
+ for (int i = 0; i < getHeight(); i++)
+ {
+ if (getSequenceAt(i) == s)
+ {
+ deleteSequence(i);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ */
+ public void deleteSequence(int i)
+ {
+ sequences.removeElementAt(i);
+ }
+
+
+ /** */
+ public SequenceGroup findGroup(SequenceI s)
+ {
+ for (int i = 0; i < this.groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+ if (sg.getSequences(false).contains(s))
+ {
+ return sg;
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceGroup[] findAllGroups(SequenceI s)
+ {
+ Vector temp = new Vector();
+
+ int gSize = groups.size();
+ for (int i = 0; i < gSize; i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ if(sg==null || sg.getSequences(false)==null)
+ {
+ this.deleteGroup(sg);
+ gSize--;
+ continue;
+ }
+
+ if (sg.getSequences(false).contains(s))
+ {
+ temp.addElement(sg);
+ }
+ }
+
+ SequenceGroup[] ret = new SequenceGroup[temp.size()];
+
+ for (int i = 0; i < temp.size(); i++)
+ {
+ ret[i] = (SequenceGroup) temp.elementAt(i);
+ }
+
+ return ret;
+ }
+
+
+
+ /** */
+ public void addGroup(SequenceGroup sg)
+ {
+ if (!groups.contains(sg))
+ {
+ groups.addElement(sg);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void deleteAllGroups()
+ {
+ groups.removeAllElements();
+
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ SequenceI s = getSequenceAt(i);
+ s.setColor(java.awt.Color.white);
+ i++;
+ }
+ }
+
+ /** */
+ public void deleteGroup(SequenceGroup g)
+ {
+ if (groups.contains(g))
+ {
+ groups.removeElement(g);
+ }
+ }
+
+ /** */
+ public SequenceI findName(String name)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i).getName().equals(name))
+ {
+ return getSequenceAt(i);
+ }
+
+ i++;
+ }
+
+ return null;
+ }
+
+
+ /** */
+ public int findIndex(SequenceI s)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (s == getSequenceAt(i))
+ {
+ return i;
+ }
+
+ i++;
+ }
+
+ return -1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getHeight()
+ {
+ return sequences.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getWidth()
+ {
+ int maxLength = -1;
+
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ if (getSequenceAt(i).getLength() > maxLength)
+ {
+ maxLength = getSequenceAt(i).getLength();
+ }
+ }
+
+ return maxLength;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getMaxIdLength()
+ {
+ int max = 0;
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ SequenceI seq = getSequenceAt(i);
+ String tmp = seq.getName() + "/" + seq.getStart() + "-" +
+ seq.getEnd();
+
+ if (tmp.length() > max)
+ {
+ max = tmp.length();
+ }
+
+ i++;
+ }
+
+ return max;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gc DOCUMENT ME!
+ */
+ public void setGapCharacter(char gc)
+ {
+ gapCharacter = gc;
+
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ Sequence seq = (Sequence) sequences.elementAt(i);
+ seq.setSequence( seq.getSequence().replace('.', gc) );
+ seq.setSequence( seq.getSequence().replace('-', gc) );
+ seq.setSequence( seq.getSequence().replace(' ', gc) );
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getGapCharacter()
+ {
+ return gapCharacter;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getAAFrequency()
+ {
+ return AAFrequency.calculate(sequences, 0, getWidth());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isAligned()
+ {
+ int width = getWidth();
+
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ if (getSequenceAt(i).getLength() != width)
+ {
+ return false;
+ }
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param aa DOCUMENT ME!
+ */
+ public void deleteAnnotation(AlignmentAnnotation aa)
+ {
+ int aSize = 1;
+
+ if (annotations != null)
+ {
+ aSize = annotations.length;
+ }
+
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+
+ int tIndex = 0;
+
+ for (int i = 0; i < aSize; i++)
+ {
+ if (annotations[i] == aa)
+ {
+ continue;
+ }
+
+ temp[tIndex] = annotations[i];
+ tIndex++;
+ }
+
+ annotations = temp;
+ }
+
+
+ public void adjustSequenceAnnotations()
+ {
+ if(annotations!=null)
+ {
+ for (int a = 0; a < annotations.length; a++)
+ {
+ if (annotations[a].sequenceRef != null)
+ {
+ annotations[a].adjustForAlignment();
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param aa DOCUMENT ME!
+ */
+ public void addAnnotation(AlignmentAnnotation aa)
+ {
+ int aSize = 1;
+ if (annotations != null)
+ {
+ aSize = annotations.length + 1;
+ }
+
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+ temp[aSize-1] = aa;
+
+ int i = 0;
+
+ if (aSize > 1)
+ {
+ for (i = 0; i < (aSize-1); i++)
+ {
+ temp[i] = annotations[i];
+ }
+ }
+
+ annotations = temp;
+ }
+
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+ {
+ if(aa==null || annotations==null || annotations.length-1<index)
+ return;
+
+ int aSize = annotations.length;
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+ temp[index] = aa;
+
+ for (int i = 0; i < aSize; i++)
+ {
+ if(i==index)
+ continue;
+
+ if(i<index)
+ temp[i] = annotations[i];
+ else
+ temp[i] = annotations[i-1];
+ }
+
+ annotations = temp;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation()
+ {
+ return annotations;
+ }
+
+ public void setNucleotide(boolean b)
+ {
+ if(b)
+ type = NUCLEOTIDE;
+ else
+ type = PROTEIN;
+ }
+
+ public boolean isNucleotide()
+ {
+ if(type==NUCLEOTIDE)
+ return true;
+ else
+ return false;
+ }
+
+ public void setDataset(Alignment data)
+ {
+ if(dataset==null && data==null)
+ {
+ // Create a new dataset for this alignment.
+ // Can only be done once, if dataset is not null
+ // This will not be performed
+ Sequence[] seqs = new Sequence[getHeight()];
+ for (int i = 0; i < getHeight(); i++)
+ {
+ if(getSequenceAt(i).getDatasetSequence()!=null)
+ {
+ seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence();
+ }
+ else
+ {
+ seqs[i] = new Sequence(getSequenceAt(i).getName(),
+ AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ getSequenceAt(i).getSequence()
+ ),
+ getSequenceAt(i).getStart(),
+ getSequenceAt(i).getEnd());
+
+ getSequenceAt(i).setDatasetSequence(seqs[i]);
+ }
+ }
+
+ dataset = new Alignment(seqs);
+ }
+ else if(dataset==null && data!=null)
+ {
+ dataset = data;
+ }
+ }
+
+ public Alignment getDataset()
+ {
+ return dataset;
+ }
+
+ public boolean padGaps() {
+ boolean modified=false;
+
+ //Remove excess gaps from the end of alignment
+ int maxLength = -1;
+
+ SequenceI current;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+ for (int j = current.getLength(); j > maxLength; j--)
+ {
+ if (j > maxLength && !jalview.util.Comparison.isGap(
+ current.getCharAt(j)))
+ {
+ maxLength = j;
+ break;
+ }
+ }
+ }
+
+ maxLength++;
+
+ for (int i = 0; i < sequences.size();
+ i++)
+ {
+ current = getSequenceAt(i);
+
+ if (current.getLength() < maxLength)
+ {
+ current.insertCharAt(maxLength - 1, gapCharacter);
+ modified=true;
+ }
+ else if(current.getLength() > maxLength)
+ {
+ current.deleteChars(maxLength, current.getLength());
+ }
+ }
+ return modified;
+ }
+
+ public HiddenSequences getHiddenSequences()
+ {
+ return hiddenSequences;
+ }
+ SequenceI [] getVisibleAndRepresentedSeqs()
+ {
+ if(hiddenSequences==null || hiddenSequences.getSize()<1)
+ return getSequencesArray();
+
+ Vector seqs = new Vector();
+ SequenceI seq;
+ SequenceGroup hidden;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ seq = (SequenceI) sequences.elementAt(i);
+ seqs.addElement(seq);
+ hidden = seq.getHiddenSequences();
+ if(hidden!=null)
+ {
+ for(int j=0; j<hidden.getSize(false); j++)
+ {
+ seqs.addElement(hidden.getSequenceAt(j));
+ }
+ }
+ }
+ SequenceI [] result = new SequenceI[seqs.size()];
+ for(int i=0; i<seqs.size(); i++)
+ result[i] = (SequenceI)seqs.elementAt(i);
+
+ return result;
+
+ }
+
+ public CigarArray getCompactAlignment()
+ {
+ SeqCigar alseqs[] = new SeqCigar[sequences.size()];
+ for (int i=0; i<sequences.size(); i++) {
+ alseqs[i] = new SeqCigar((SequenceI) sequences.get(i));
+ }
+ return new CigarArray(alseqs);
+ }
+
+}
-/*\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 java.util.*;\r
-\r
-/**\r
- * NOTE: Columns are zero based.\r
- */\r
-public class ColumnSelection\r
-{\r
- Vector selected = new Vector();\r
-\r
- //Vector of int [] {startCol, endCol}\r
- Vector hiddenColumns;\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param col DOCUMENT ME!\r
- */\r
- public void addElement(int col)\r
- {\r
- if (!selected.contains(new Integer(col)))\r
- {\r
- selected.addElement(new Integer(col));\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void clear()\r
- {\r
- selected.removeAllElements();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param col DOCUMENT ME!\r
- */\r
- public void removeElement(int col)\r
- {\r
- Integer colInt = new Integer(col);\r
-\r
- if (selected.contains(colInt))\r
- {\r
- selected.removeElement(colInt);\r
- }\r
- }\r
-\r
- public void removeElements(int start, int end)\r
- {\r
- Integer colInt;\r
- for(int i=start; i<end; i++)\r
- {\r
- colInt = new Integer(i);\r
- if (selected.contains(colInt))\r
- {\r
- selected.removeElement(colInt);\r
- }\r
- }\r
- }\r
-\r
- public Vector getSelected()\r
- {\r
- return selected;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param col DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean contains(int col)\r
- {\r
- return selected.contains(new Integer(col));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int columnAt(int i)\r
- {\r
- return ((Integer) selected.elementAt(i)).intValue();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int size()\r
- {\r
- return selected.size();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getMax()\r
- {\r
- int max = -1;\r
-\r
- for (int i = 0; i < selected.size(); i++)\r
- {\r
- if (columnAt(i) > max)\r
- {\r
- max = columnAt(i);\r
- }\r
- }\r
-\r
- return max;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getMin()\r
- {\r
- int min = 1000000000;\r
-\r
- for (int i = 0; i < selected.size(); i++)\r
- {\r
- if (columnAt(i) < min)\r
- {\r
- min = columnAt(i);\r
- }\r
- }\r
-\r
- return min;\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param start DOCUMENT ME!\r
- * @param change DOCUMENT ME!\r
- */\r
- public void compensateForEdit(int start, int change)\r
- {\r
- for (int i = 0; i < size(); i++)\r
- {\r
- int temp = columnAt(i);\r
-\r
- if (temp >= start)\r
- {\r
- selected.setElementAt(new Integer(temp - change), i);\r
- }\r
- }\r
-\r
- if(hiddenColumns!=null)\r
- {\r
- for(int i=0; i<hiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(i);\r
- if(region[0] > start)\r
- {\r
- region[0] -= change;\r
- region[1] -= change;\r
- }\r
- if(region[0]<0)\r
- region[0] = 0;\r
- if(region[1] <0)\r
- region[1] = 0;\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * This Method is used to return all the HiddenColumn regions\r
- * less than the given index.\r
- * @param end int\r
- * @return Vector\r
- */\r
- public Vector getHiddenColumns()\r
- {\r
- return hiddenColumns;\r
- }\r
-\r
- public int adjustForHiddenColumns(int column)\r
- {\r
- int result = column;\r
- if (hiddenColumns != null)\r
- {\r
- for (int i = 0; i < hiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(i);\r
- if (result >= region[0])\r
- {\r
- result += region[1] - region[0] + 1;\r
- }\r
- }\r
- }\r
- return result;\r
- }\r
-\r
- /**\r
- * Use this method to find out where a visible column is in the alignment\r
- * when hidden columns exist\r
- * @param hiddenColumn int\r
- * @return int\r
- */\r
- public int findColumnPosition(int hiddenColumn)\r
- {\r
- int result = hiddenColumn;\r
- if (hiddenColumns != null)\r
- {\r
- int index = 0;\r
- int gaps = 0;\r
- do\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(index);\r
- if (hiddenColumn > region[1])\r
- {\r
- result -= region[1]+1-region[0];\r
- }\r
- index++;\r
- }\r
- while (index < hiddenColumns.size());\r
-\r
- result -= gaps;\r
- }\r
-\r
- return result;\r
- }\r
-\r
- /**\r
- * Use this method to determine where the next hiddenRegion starts\r
- */\r
- public int findHiddenRegionPosition(int hiddenRegion)\r
- {\r
- int result = 0;\r
- if (hiddenColumns != null)\r
- {\r
- int index = 0;\r
- int gaps = 0;\r
- do\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(index);\r
- if(hiddenRegion==0)\r
- {\r
- return region[0];\r
- }\r
-\r
- gaps += region[1] +1 - region[0];\r
- result = region[1] +1;\r
- index++;\r
- }\r
- while(index < hiddenRegion+1);\r
-\r
- result -= gaps;\r
- }\r
-\r
- return result;\r
- }\r
-\r
- /**\r
- * THis method returns the rightmost limit of a\r
- * region of an alignment with hidden columns.\r
- * In otherwords, the next hidden column.\r
- * @param index int\r
- */\r
- public int getHiddenBoundaryRight(int alPos)\r
- {\r
- if (hiddenColumns != null)\r
- {\r
- int index = 0;\r
- do\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(index);\r
- if(alPos < region[0])\r
- return region[0];\r
-\r
- index++;\r
- }\r
- while(index < hiddenColumns.size());\r
- }\r
-\r
- return alPos;\r
-\r
- }\r
- /**\r
- * THis method returns the rightmost limit of a\r
- * region of an alignment with hidden columns.\r
- * In otherwords, the next hidden column.\r
- * @param index int\r
- */\r
- public int getHiddenBoundaryLeft(int alPos)\r
- {\r
- if (hiddenColumns != null)\r
- {\r
- int index = hiddenColumns.size()-1;\r
- do\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(index);\r
- if(alPos > region[1])\r
- return region[1];\r
-\r
- index--;\r
- }\r
- while(index >-1);\r
- }\r
-\r
- return alPos;\r
- }\r
-\r
- public void hideSelectedColumns()\r
- {\r
- while (size() > 0)\r
- {\r
- int column = ( (Integer) getSelected().firstElement()).intValue();\r
- hideColumns(column);\r
- }\r
-\r
- }\r
-\r
- public void hideColumns(int start, int end)\r
- {\r
- if(hiddenColumns==null)\r
- hiddenColumns = new Vector();\r
-\r
- boolean added = false;\r
- boolean overlap = false;\r
-\r
- for (int i = 0; i < hiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(i);\r
- if ( start<=region[1] && end>=region[0])\r
- {\r
- hiddenColumns.removeElementAt(i);\r
- overlap = true;\r
- break;\r
- }\r
- else if (end < region[0] && start < region[0])\r
- {\r
- hiddenColumns.insertElementAt(new int[]\r
- {start, end}, i);\r
- added = true;\r
- break;\r
- }\r
- }\r
-\r
- if(overlap)\r
- {\r
- hideColumns(start, end);\r
- }\r
- else if (!added)\r
- hiddenColumns.addElement(new int[] {start, end});\r
-\r
- }\r
-\r
- /**\r
- * This method will find a range of selected columns\r
- * around the column specified\r
- * @param res int\r
- */\r
- public void hideColumns(int col)\r
- {\r
- // First find out range of columns to hide\r
- int min = col, max = col+1;\r
- while( contains(min) )\r
- { removeElement(min); min --; }\r
-\r
- while( contains(max) )\r
- { removeElement(max); max ++; }\r
-\r
- min++; max--;\r
-\r
- hideColumns(min, max);\r
- }\r
-\r
- public void revealAllHiddenColumns()\r
- {\r
- if(hiddenColumns!=null)\r
- {\r
- for (int i = 0; i < hiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(i);\r
- for (int j = region[0]; j < region[1]; j++)\r
- {\r
- addElement(j);\r
- }\r
- }\r
- }\r
-\r
- hiddenColumns = null;\r
- }\r
-\r
- public void revealHiddenColumns(int res)\r
- {\r
- for(int i=0; i<hiddenColumns.size(); i++)\r
- {\r
- int [] region = (int[])hiddenColumns.elementAt(i);\r
- if( res == region[0])\r
- {\r
- for (int j = region[0]; j < region[1]; j++)\r
- {\r
- addElement(j);\r
- }\r
-\r
- hiddenColumns.removeElement(region);\r
- break;\r
- }\r
- }\r
- if(hiddenColumns.size()==0)\r
- hiddenColumns = null;\r
- }\r
-\r
- public boolean isVisible(int column)\r
- {\r
- for(int i=0; i<hiddenColumns.size(); i++)\r
- {\r
- int [] region = (int[])hiddenColumns.elementAt(i);\r
- if( column >= region[0] && column <= region[1])\r
- {\r
- return false;\r
- }\r
- }\r
- return true;\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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.*;
+
+/**
+ * NOTE: Columns are zero based.
+ */
+public class ColumnSelection
+{
+ Vector selected = new Vector();
+
+ //Vector of int [] {startCol, endCol}
+ Vector hiddenColumns;
+
+ /**
+ * Add a column to the selection
+ *
+ * @param col index of column
+ */
+ public void addElement(int col)
+ {
+ Integer column = new Integer(col);
+ if (!selected.contains(column))
+ {
+ selected.addElement(column);
+ }
+ }
+
+ /**
+ * clears column selection
+ */
+ public void clear()
+ {
+ selected.removeAllElements();
+ }
+
+ /**
+ * removes col from selection
+ *
+ * @param col index of column to be removed
+ */
+ public void removeElement(int col)
+ {
+ Integer colInt = new Integer(col);
+
+ if (selected.contains(colInt))
+ {
+ selected.removeElement(colInt);
+ }
+ }
+
+ /**
+ * removes a range of columns from the selection
+ * @param start int - first column in range to be removed
+ * @param end int - last col
+ */
+ public void removeElements(int start, int end)
+ {
+ Integer colInt;
+ for(int i=start; i<end; i++)
+ {
+ colInt = new Integer(i);
+ if (selected.contains(colInt))
+ {
+ selected.removeElement(colInt);
+ }
+ }
+ }
+ /**
+ *
+ * @return Vector containing selected columns as Integers
+ */
+ public Vector getSelected()
+ {
+ return selected;
+ }
+
+ /**
+ *
+ * @param col index to search for in column selection
+ *
+ * @return true if Integer(col) is in selection.
+ */
+ public boolean contains(int col)
+ {
+ return selected.contains(new Integer(col));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int columnAt(int i)
+ {
+ return ((Integer) selected.elementAt(i)).intValue();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int size()
+ {
+ return selected.size();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getMax()
+ {
+ int max = -1;
+
+ for (int i = 0; i < selected.size(); i++)
+ {
+ if (columnAt(i) > max)
+ {
+ max = columnAt(i);
+ }
+ }
+
+ return max;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getMin()
+ {
+ int min = 1000000000;
+
+ for (int i = 0; i < selected.size(); i++)
+ {
+ if (columnAt(i) < min)
+ {
+ min = columnAt(i);
+ }
+ }
+
+ return min;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start DOCUMENT ME!
+ * @param change DOCUMENT ME!
+ */
+ public void compensateForEdit(int start, int change)
+ {
+ for (int i = 0; i < size(); i++)
+ {
+ int temp = columnAt(i);
+
+ if (temp >= start)
+ {
+ selected.setElementAt(new Integer(temp - change), i);
+ }
+ }
+
+ if(hiddenColumns!=null)
+ {
+ for(int i=0; i<hiddenColumns.size(); i++)
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(i);
+ if(region[0] > start)
+ {
+ region[0] -= change;
+ region[1] -= change;
+ }
+ if(region[0]<0)
+ region[0] = 0;
+ if(region[1] <0)
+ region[1] = 0;
+ }
+ }
+ }
+
+ /**
+ * This Method is used to return all the HiddenColumn regions
+ * less than the given index.
+ * @param end int
+ * @return Vector
+ */
+ public Vector getHiddenColumns()
+ {
+ return hiddenColumns;
+ }
+ /**
+ * Return absolute column index for a visible column index
+ * @param column int column index in alignment view
+ * @return alignment column index for column
+ */
+ public int adjustForHiddenColumns(int column)
+ {
+ int result = column;
+ if (hiddenColumns != null)
+ {
+ for (int i = 0; i < hiddenColumns.size(); i++)
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(i);
+ if (result >= region[0])
+ {
+ result += region[1] - region[0] + 1;
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Use this method to find out where a visible column is in the alignment
+ * when hidden columns exist
+ * @param hiddenColumn int
+ * @return int
+ */
+ public int findColumnPosition(int hiddenColumn)
+ {
+ int result = hiddenColumn;
+ if (hiddenColumns != null)
+ {
+ int index = 0;
+ int gaps = 0;
+ do
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(index);
+ if (hiddenColumn > region[1])
+ {
+ result -= region[1]+1-region[0];
+ }
+ index++;
+ }
+ while (index < hiddenColumns.size());
+
+ result -= gaps;
+ }
+
+ return result;
+ }
+
+ /**
+ * Use this method to determine where the next hiddenRegion starts
+ */
+ public int findHiddenRegionPosition(int hiddenRegion)
+ {
+ int result = 0;
+ if (hiddenColumns != null)
+ {
+ int index = 0;
+ int gaps = 0;
+ do
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(index);
+ if(hiddenRegion==0)
+ {
+ return region[0];
+ }
+
+ gaps += region[1] +1 - region[0];
+ result = region[1] +1;
+ index++;
+ }
+ while(index < hiddenRegion+1);
+
+ result -= gaps;
+ }
+
+ return result;
+ }
+
+ /**
+ * THis method returns the rightmost limit of a
+ * region of an alignment with hidden columns.
+ * In otherwords, the next hidden column.
+ * @param index int
+ */
+ public int getHiddenBoundaryRight(int alPos)
+ {
+ if (hiddenColumns != null)
+ {
+ int index = 0;
+ do
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(index);
+ if(alPos < region[0])
+ return region[0];
+
+ index++;
+ }
+ while(index < hiddenColumns.size());
+ }
+
+ return alPos;
+
+ }
+ /**
+ * THis method returns the rightmost limit of a
+ * region of an alignment with hidden columns.
+ * In otherwords, the next hidden column.
+ * @param index int
+ */
+ public int getHiddenBoundaryLeft(int alPos)
+ {
+ if (hiddenColumns != null)
+ {
+ int index = hiddenColumns.size()-1;
+ do
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(index);
+ if(alPos > region[1])
+ return region[1];
+
+ index--;
+ }
+ while(index >-1);
+ }
+
+ return alPos;
+
+ }
+
+ public void hideSelectedColumns()
+ {
+ while (size() > 0)
+ {
+ int column = ( (Integer) getSelected().firstElement()).intValue();
+ hideColumns(column);
+ }
+
+ }
+
+ public void hideColumns(int start, int end)
+ {
+ if(hiddenColumns==null)
+ hiddenColumns = new Vector();
+
+ boolean added = false;
+ boolean overlap = false;
+
+ for (int i = 0; i < hiddenColumns.size(); i++)
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(i);
+ if ( start<=region[1] && end>=region[0])
+ {
+ hiddenColumns.removeElementAt(i);
+ overlap = true;
+ break;
+ }
+ else if (end < region[0] && start < region[0])
+ {
+ hiddenColumns.insertElementAt(new int[]
+ {start, end}, i);
+ added = true;
+ break;
+ }
+ }
+
+ if(overlap)
+ {
+ hideColumns(start, end);
+ }
+ else if (!added)
+ hiddenColumns.addElement(new int[] {start, end});
+
+ }
+
+ /**
+ * This method will find a range of selected columns
+ * around the column specified
+ * @param res int
+ */
+ public void hideColumns(int col)
+ {
+ // First find out range of columns to hide
+ int min = col, max = col+1;
+ while( contains(min) )
+ { removeElement(min); min --; }
+
+ while( contains(max) )
+ { removeElement(max); max ++; }
+
+ min++; max--;
+
+ hideColumns(min, max);
+ }
+
+ public void revealAllHiddenColumns()
+ {
+ if(hiddenColumns!=null)
+ {
+ for (int i = 0; i < hiddenColumns.size(); i++)
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(i);
+ for (int j = region[0]; j < region[1]; j++)
+ {
+ addElement(j);
+ }
+ }
+ }
+
+ hiddenColumns = null;
+ }
+
+ public void revealHiddenColumns(int res)
+ {
+ for(int i=0; i<hiddenColumns.size(); i++)
+ {
+ int [] region = (int[])hiddenColumns.elementAt(i);
+ if( res == region[0])
+ {
+ for (int j = region[0]; j < region[1]; j++)
+ {
+ addElement(j);
+ }
+
+ hiddenColumns.removeElement(region);
+ break;
+ }
+ }
+ if(hiddenColumns.size()==0)
+ hiddenColumns = null;
+ }
+
+ public boolean isVisible(int column)
+ {
+ for(int i=0; i<hiddenColumns.size(); i++)
+ {
+ int [] region = (int[])hiddenColumns.elementAt(i);
+ if( column >= region[0] && column <= region[1])
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff