-/*\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
-\r
-/** Data structure to hold and manipulate a multiple sequence alignment\r
- */\r
-public class Alignment implements AlignmentI\r
-{\r
- protected Vector sequences;\r
- protected Vector groups = new Vector();\r
- protected Vector superGroup = new Vector();\r
- protected char gapCharacter = '-';\r
-\r
- /** DOCUMENT ME!! */\r
- public AlignmentAnnotation[] annotations;\r
-\r
- /** DOCUMENT ME!! */\r
- public boolean featuresAdded = false;\r
-\r
- /** Make an alignment from an array of Sequences.\r
- *\r
- * @param sequences\r
- */\r
- public Alignment(SequenceI[] seqs)\r
- {\r
- sequences = new Vector();\r
-\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- sequences.addElement(seqs[i]);\r
- }\r
-\r
- getWidth();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getSequences()\r
- {\r
- return sequences;\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
- sequences.addElement(snew);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq DOCUMENT ME!\r
- */\r
- public void addSequence(SequenceI[] seq)\r
- {\r
- for (int i = 0; i < seq.length; i++)\r
- {\r
- addSequence(seq[i]);\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 current;\r
- int iSize = getWidth();\r
-\r
- for (int i = 0; i < iSize; i++)\r
- {\r
- boolean delete = true;\r
-\r
- for (int j = 0; j < getHeight(); j++)\r
- {\r
- current = getSequenceAt(j);\r
-\r
- if (current.getLength() > i)\r
- {\r
- /* MC Should move this to a method somewhere */\r
- if (!jalview.util.Comparison.isGap(current.getCharAt(i)))\r
- {\r
- delete = false;\r
- }\r
- }\r
- }\r
-\r
- if (delete)\r
- {\r
- deleteColumns(i, i);\r
- iSize--;\r
- i--;\r
- }\r
- }\r
- }\r
-\r
- /** Removes a range of columns (start to end inclusive).\r
- *\r
- * @param start Start column in the alignment\r
- * @param end End column in the alignment\r
- */\r
- public void deleteColumns(int start, int end)\r
- {\r
- deleteColumns(0, getHeight() - 1, start, end);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq1 DOCUMENT ME!\r
- * @param seq2 DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- */\r
- public void deleteColumns(int seq1, int seq2, int start, int end)\r
- {\r
- for (int i = 0; i <= (end - start); i++)\r
- {\r
- for (int j = seq1; j <= seq2; j++)\r
- {\r
- getSequenceAt(j).deleteCharAt(start);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- public void trimLeft(int i)\r
- {\r
- for (int j = 0; j < getHeight(); j++)\r
- {\r
- SequenceI s = getSequenceAt(j);\r
- int newstart = s.findPosition(i);\r
-\r
- s.setStart(newstart);\r
- s.setSequence(s.getSequence().substring(i));\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- public void trimRight(int i)\r
- {\r
- for (int j = 0; j < getHeight(); j++)\r
- {\r
- SequenceI s = getSequenceAt(j);\r
- int newend = s.findPosition(i);\r
-\r
- s.setEnd(newend);\r
- s.setSequence(s.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
- * DOCUMENT ME!\r
- *\r
- * @param threshold DOCUMENT ME!\r
- * @param sel DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector removeRedundancy(float threshold, Vector sel)\r
- {\r
- Vector del = new Vector();\r
-\r
- for (int i = 1; i < sel.size(); i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\r
- // Only do the comparison if either have not been deleted\r
- if (!del.contains((SequenceI) sel.elementAt(i)) ||\r
- !del.contains((SequenceI) sel.elementAt(j)))\r
- {\r
- // use PID instead of Comparison (which is really not pleasant)\r
- float pid = Comparison.PID((SequenceI) sel.elementAt(j),\r
- (SequenceI) sel.elementAt(i));\r
-\r
- if (pid >= threshold)\r
- {\r
- // Delete the shortest one\r
- if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel\r
- .elementAt(\r
- i)).getSequence().length())\r
- {\r
- del.addElement(sel.elementAt(i));\r
- }\r
- else\r
- {\r
- del.addElement(sel.elementAt(i));\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- // Now delete the sequences\r
- for (int i = 0; i < del.size(); i++)\r
- {\r
- deleteSequence((SequenceI) del.elementAt(i));\r
- }\r
-\r
- return del;\r
- }\r
-\r
- /** */\r
- public SequenceGroup findGroup(int i)\r
- {\r
- return findGroup(getSequenceAt(i));\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.sequences.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.sequences==null)\r
- {\r
- this.deleteGroup(sg);\r
- gSize--;\r
- continue;\r
- }\r
-\r
- if (sg.sequences.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
- * DOCUMENT ME!\r
- *\r
- * @param sg DOCUMENT ME!\r
- */\r
- public void addSuperGroup(SuperGroup sg)\r
- {\r
- superGroup.addElement(sg);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param sg DOCUMENT ME!\r
- */\r
- public void removeSuperGroup(SuperGroup sg)\r
- {\r
- superGroup.removeElement(sg);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param sg DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SuperGroup getSuperGroup(SequenceGroup sg)\r
- {\r
- for (int i = 0; i < this.superGroup.size(); i++)\r
- {\r
- SuperGroup temp = (SuperGroup) superGroup.elementAt(i);\r
-\r
- if (temp.sequenceGroups.contains(sg))\r
- {\r
- return temp;\r
- }\r
- }\r
-\r
- return null;\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
- superGroup.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
- SequenceI s = getSequenceAt(i);\r
-\r
- if (s.getName().equals(name))\r
- {\r
- return s;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /** */\r
- public SequenceI findbyDisplayId(String name)\r
- {\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- SequenceI s = getSequenceAt(i);\r
-\r
- if (s.getDisplayId().equals(name))\r
- {\r
- return s;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return null;\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.sequence = seq.sequence.replace('.', gc);\r
- seq.sequence = seq.sequence.replace('-', gc);\r
- seq.sequence = seq.sequence.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
- * DOCUMENT ME!\r
- *\r
- * @param aa DOCUMENT ME!\r
- */\r
- public void addAnnotation(AlignmentAnnotation aa)\r
- {\r
- int aSize = 1;\r
-\r
- if (annotations != null)\r
- {\r
- aSize = annotations.length + 1;\r
- }\r
-\r
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\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
- temp[i] = aa;\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
+/*
+ * 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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff