-/*\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
- protected Vector sequences;\r
- protected Vector groups = new Vector();\r
- protected Vector superGroup = new Vector();\r
- protected char gapCharacter = '-';\r
- public AlignmentAnnotation[] annotations;\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
- sequences = new Vector();\r
-\r
- for (int i = 0; i < seqs.length; i++)\r
- sequences.addElement(seqs[i]);\r
-\r
- getWidth();\r
- }\r
-\r
- public Vector getSequences() {\r
- return sequences;\r
- }\r
-\r
- public SequenceI getSequenceAt(int i) {\r
- if (i < sequences.size()) {\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
- sequences.addElement(snew);\r
- }\r
-\r
- public void addSequence(SequenceI[] seq) {\r
- for (int i = 0; i < seq.length; i++) {\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
- SequenceI oldseq = getSequenceAt(i);\r
- deleteSequence(oldseq);\r
-\r
- sequences.setElementAt(snew, i);\r
- }\r
-\r
- public Vector getGroups() {\r
- return groups;\r
- }\r
-\r
- /** Sorts the sequences by sequence group size - largest to smallest.\r
- * Uses QuickSort.\r
- */\r
- public void sortGroups() {\r
- float[] arr = new float[groups.size()];\r
- Object[] s = new Object[groups.size()];\r
-\r
- for (int i = 0; i < groups.size(); i++) {\r
- arr[i] = ((SequenceGroup) groups.elementAt(i)).sequences.size();\r
- s[i] = groups.elementAt(i);\r
- }\r
-\r
- QuickSort.sort(arr, s);\r
-\r
- Vector newg = new Vector(groups.size());\r
-\r
- for (int i = groups.size() - 1; i >= 0; i--) {\r
- newg.addElement(s[i]);\r
- }\r
-\r
- groups = newg;\r
- }\r
-\r
- /** Takes out columns consisting entirely of gaps (-,.," ")\r
- */\r
- public void removeGaps() {\r
- SequenceI current;\r
- int iSize = getWidth();\r
-\r
- for (int i = 0; i < iSize; i++) {\r
- boolean delete = true;\r
-\r
- for (int j = 0; j < getHeight(); j++) {\r
- current = getSequenceAt(j);\r
-\r
- if (current.getLength() > i) {\r
- /* MC Should move this to a method somewhere */\r
- if (!jalview.util.Comparison.isGap(current.getCharAt(i))) {\r
- delete = false;\r
- }\r
- }\r
- }\r
-\r
- if (delete) {\r
- deleteColumns(i, i);\r
- iSize--;\r
- i--;\r
- }\r
- }\r
- }\r
-\r
- /** Returns an array of Sequences containing columns\r
- * start to end (inclusive) only.\r
- *\r
- * @param start start column to fetch\r
- * @param end end column to fetch\r
- * @return Array of Sequences, ready to put into a new Alignment\r
- */\r
- public SequenceI[] getColumns(int start, int end) {\r
- return getColumns(0, getHeight() - 1, start, end);\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
- deleteColumns(0, getHeight() - 1, start, end);\r
- }\r
-\r
- public void deleteColumns(int seq1, int seq2, int start, int end) {\r
- for (int i = 0; i <= (end - start); i++) {\r
- for (int j = seq1; j <= seq2; j++) {\r
- getSequenceAt(j).deleteCharAt(start);\r
- }\r
- }\r
- }\r
-\r
- public void insertColumns(SequenceI[] seqs, int pos) {\r
- if (seqs.length == getHeight()) {\r
- for (int i = 0; i < getHeight(); i++) {\r
- String tmp = new String(getSequenceAt(i).getSequence());\r
- getSequenceAt(i).setSequence(tmp.substring(0, pos) +\r
- seqs[i].getSequence() + tmp.substring(pos));\r
- }\r
- }\r
- }\r
-\r
- public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {\r
- SequenceI[] seqs = new Sequence[(seq2 - seq1) + 1];\r
-\r
- for (int i = seq1; i <= seq2; i++) {\r
- seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
- getSequenceAt(i).getSequence().substring(start, end),\r
- getSequenceAt(i).findPosition(start),\r
- getSequenceAt(i).findPosition(end));\r
- }\r
-\r
- return seqs;\r
- }\r
-\r
- public void trimLeft(int i) {\r
- for (int j = 0; j < getHeight(); j++) {\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
- public void trimRight(int i) {\r
- for (int j = 0; j < getHeight(); j++) {\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
- public void deleteSequence(SequenceI s) {\r
- for (int i = 0; i < getHeight(); i++)\r
- if (getSequenceAt(i) == s) {\r
- deleteSequence(i);\r
- }\r
- }\r
-\r
- public void deleteSequence(int i) {\r
- sequences.removeElementAt(i);\r
- }\r
-\r
- public Vector removeRedundancy(float threshold, Vector sel) {\r
- Vector del = new Vector();\r
-\r
- for (int i = 1; i < sel.size(); i++) {\r
- for (int j = 0; j < i; j++) {\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
- // 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
- // Delete the shortest one\r
- if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel\r
- .elementAt(\r
- i)).getSequence().length()) {\r
- del.addElement(sel.elementAt(i));\r
- } else {\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
- deleteSequence((SequenceI) del.elementAt(i));\r
-\r
- return del;\r
- }\r
-\r
- public void sortByPID(SequenceI s) {\r
- float[] scores = new float[getHeight()];\r
- SequenceI[] seqs = new SequenceI[getHeight()];\r
-\r
- for (int i = 0; i < getHeight(); i++) {\r
- scores[i] = Comparison.compare(getSequenceAt(i), s);\r
- seqs[i] = getSequenceAt(i);\r
- }\r
-\r
- QuickSort.sort(scores, 0, scores.length - 1, seqs);\r
-\r
- int len = 0;\r
-\r
- if ((getHeight() % 2) == 0) {\r
- len = getHeight() / 2;\r
- } else {\r
- len = (getHeight() + 1) / 2;\r
- }\r
-\r
- for (int i = 0; i < len; i++) {\r
- SequenceI tmp = seqs[i];\r
- sequences.setElementAt(seqs[getHeight() - i - 1], i);\r
- sequences.setElementAt(tmp, getHeight() - i - 1);\r
- }\r
- }\r
-\r
- public void sortByID() {\r
- String[] ids = new String[getHeight()];\r
- SequenceI[] seqs = new SequenceI[getHeight()];\r
-\r
- for (int i = 0; i < getHeight(); i++) {\r
- ids[i] = getSequenceAt(i).getName();\r
- seqs[i] = getSequenceAt(i);\r
- }\r
-\r
- QuickSort.sort(ids, seqs);\r
-\r
- int len = 0;\r
-\r
- if ((getHeight() % 2) == 0) {\r
- len = getHeight() / 2;\r
- } else {\r
- len = (getHeight() + 1) / 2;\r
- System.out.println("DEBUG:Sort len is odd = " + len); // log.\r
- }\r
-\r
- for (int i = 0; i < len; i++) {\r
- System.out.println("DEBUG:Swapping " + seqs[i].getName() + " and " +\r
- seqs[getHeight() - i - 1].getName()); // log.\r
-\r
- SequenceI tmp = seqs[i];\r
- sequences.setElementAt(seqs[getHeight() - i - 1], i);\r
- sequences.setElementAt(tmp, getHeight() - i - 1);\r
- }\r
- }\r
-\r
- /** */\r
- public SequenceGroup findGroup(int i) {\r
- return findGroup(getSequenceAt(i));\r
- }\r
-\r
- /** */\r
- public SequenceGroup findGroup(SequenceI s) {\r
- for (int i = 0; i < this.groups.size(); i++) {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
- if (sg.sequences.contains(s)) {\r
- return sg;\r
- }\r
- }\r
-\r
- return null;\r
- }\r
-\r
- public SequenceGroup[] findAllGroups(SequenceI s) {\r
- Vector temp = new Vector();\r
-\r
- for (int i = 0; i < this.groups.size(); i++) {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
- if (sg.sequences.contains(s)) {\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
- ret[i] = (SequenceGroup) temp.elementAt(i);\r
-\r
- return ret;\r
- }\r
-\r
- /** */\r
- public void addToGroup(SequenceGroup g, SequenceI s) {\r
- if (!(g.sequences.contains(s))) {\r
- g.sequences.addElement(s);\r
- }\r
- }\r
-\r
- /** */\r
- public void removeFromGroup(SequenceGroup g, SequenceI s) {\r
- if ((g != null) && (g.sequences != null)) {\r
- if (g.sequences.contains(s)) {\r
- g.sequences.removeElement(s);\r
-\r
- if (g.sequences.size() == 0) {\r
- groups.removeElement(g);\r
- }\r
- }\r
- }\r
- }\r
-\r
- public void addSuperGroup(SuperGroup sg) {\r
- superGroup.addElement(sg);\r
- }\r
-\r
- public void removeSuperGroup(SuperGroup sg) {\r
- superGroup.removeElement(sg);\r
- }\r
-\r
- public SuperGroup getSuperGroup(SequenceGroup sg) {\r
- for (int i = 0; i < this.superGroup.size(); i++) {\r
- SuperGroup temp = (SuperGroup) superGroup.elementAt(i);\r
-\r
- if (temp.sequenceGroups.contains(sg)) {\r
- return temp;\r
- }\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /** */\r
- public void addGroup(SequenceGroup sg) {\r
- if (!groups.contains(sg)) {\r
- groups.addElement(sg);\r
- }\r
- }\r
-\r
- public void deleteAllGroups() {\r
- groups.removeAllElements();\r
- superGroup.removeAllElements();\r
-\r
- int i = 0;\r
-\r
- while (i < sequences.size()) {\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
- if (groups.contains(g)) {\r
- groups.removeElement(g);\r
- }\r
- }\r
-\r
- /** */\r
- public SequenceI findName(String name) {\r
- int i = 0;\r
-\r
- while (i < sequences.size()) {\r
- SequenceI s = getSequenceAt(i);\r
-\r
- if (s.getName().equals(name)) {\r
- return s;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /** */\r
- public SequenceI findbyDisplayId(String name) {\r
- int i = 0;\r
-\r
- while (i < sequences.size()) {\r
- SequenceI s = getSequenceAt(i);\r
-\r
- if (s.getDisplayId().equals(name)) {\r
- return s;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /** */\r
- public int findIndex(SequenceI s) {\r
- int i = 0;\r
-\r
- while (i < sequences.size()) {\r
- if (s == getSequenceAt(i)) {\r
- return i;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return -1;\r
- }\r
-\r
- public int getHeight() {\r
- return sequences.size();\r
- }\r
-\r
- public int getWidth() {\r
- int maxLength = -1;\r
-\r
- for (int i = 0; i < sequences.size(); i++) {\r
- if (getSequenceAt(i).getLength() > maxLength) {\r
- maxLength = getSequenceAt(i).getLength();\r
- }\r
- }\r
-\r
- return maxLength;\r
- }\r
-\r
- public int getMaxIdLength() {\r
- int max = 0;\r
- int i = 0;\r
-\r
- while (i < sequences.size()) {\r
- SequenceI seq = getSequenceAt(i);\r
- String tmp = seq.getName() + "/" + seq.getStart() + "-" +\r
- seq.getEnd();\r
-\r
- if (tmp.length() > max) {\r
- max = tmp.length();\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return max;\r
- }\r
-\r
- public void setGapCharacter(char gc) {\r
- gapCharacter = gc;\r
-\r
- for (int i = 0; i < sequences.size(); i++) {\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
- public char getGapCharacter() {\r
- return gapCharacter;\r
- }\r
-\r
- public Vector getAAFrequency() {\r
- return AAFrequency.calculate(sequences, 0, getWidth());\r
- }\r
-\r
- public boolean isAligned() {\r
- int width = getWidth();\r
-\r
- for (int i = 0; i < sequences.size(); i++)\r
- if (getSequenceAt(i).getLength() != width) {\r
- return false;\r
- }\r
-\r
- return true;\r
- }\r
-\r
- public void deleteAnnotation(AlignmentAnnotation aa) {\r
- int aSize = 1;\r
-\r
- if (annotations != null) {\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
- if (annotations[i] == aa) {\r
- continue;\r
- }\r
-\r
- temp[tIndex] = annotations[i];\r
- tIndex++;\r
- }\r
-\r
- annotations = temp;\r
- }\r
-\r
- public void addAnnotation(AlignmentAnnotation aa) {\r
- int aSize = 1;\r
-\r
- if (annotations != null) {\r
- aSize = annotations.length + 1;\r
- }\r
-\r
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
- int i = 0;\r
-\r
- if (aSize > 1) {\r
- for (i = 0; i < (aSize - 1); i++)\r
- temp[i] = annotations[i];\r
- }\r
-\r
- temp[i] = aa;\r
-\r
- annotations = temp;\r
- }\r
-\r
- public AlignmentAnnotation[] getAlignmentAnnotation() {\r
- return annotations;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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 = SeqCigar.createAlignmentSequences(alseqs, gapCharacter, new ColumnSelection(), null);
+ 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 static AlignmentI createAlignment(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)
+ {
+ getDataset().addSequence(snew.getDatasetSequence());
+ }
+ else
+ {
+ Sequence ds = new Sequence(snew.getName(),
+ AlignSeq.extractGaps("-. ",
+ snew.getSequenceAsString()),
+ snew.getStart(),
+ snew.getEnd());
+
+ snew.setDatasetSequence(ds);
+ getDataset().addSequence(ds);
+ }
+ }
+ sequences.addElement(snew);
+
+ hiddenSequences.adjustHeightSequenceAdded();
+ }
+
+
+ /** 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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ */
+ public void deleteSequence(SequenceI s)
+ {
+ deleteSequence(findIndex(s));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ */
+ public void deleteSequence(int i)
+ {
+ if(i>-1 && i<getHeight())
+ {
+ sequences.removeElementAt(i);
+ hiddenSequences.adjustHeightSequenceDeleted(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))
+ {
+ if(hiddenSequences.getSize()>0)
+ {
+ //We're not going to make groups of
+ //Hidden sequences
+ int i, iSize = sg.getSize(false);
+ for (i = 0; i < iSize; i++)
+ {
+ if (!sequences.contains(sg.getSequenceAt(i)))
+ {
+ sg.deleteSequence(sg.getSequenceAt(i), false);
+ iSize--;
+ i--;
+ }
+ }
+
+ if (sg.getSize(true) < 1)
+ return;
+ }
+
+ groups.addElement(sg);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void deleteAllGroups()
+ {
+ groups.removeAllElements();
+ }
+
+ /** */
+ 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 SequenceI [] findSequenceMatch(String name)
+ {
+ Vector matches = new Vector();
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i).getName().equals(name))
+ {
+ matches.addElement(getSequenceAt(i));
+ }
+ i++;
+ }
+
+ SequenceI [] result = new SequenceI[matches.size()];
+ for(i=0; i<result.length; i++)
+ result[i] = (SequenceI)matches.elementAt(i);
+
+ return result;
+
+ }
+
+
+ /** */
+ 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!
+ *
+ * @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.getSequenceAsString().replace('.', gc) );
+ seq.setSequence( seq.getSequenceAsString().replace('-', gc) );
+ seq.setSequence( seq.getSequenceAsString().replace(' ', gc) );
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getGapCharacter()
+ {
+ return gapCharacter;
+ }
+
+
+ /**
+ * 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;
+ }
+
+ if(aSize<1)
+ return;
+
+ 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()];
+ SequenceI currentSeq;
+ for (int i = 0; i < getHeight(); i++)
+ {
+ currentSeq = getSequenceAt(i);
+ if(currentSeq.getDatasetSequence()!=null)
+ {
+ seqs[i] = (Sequence)currentSeq.getDatasetSequence();
+ }
+ else
+ {
+ seqs[i] = new Sequence(currentSeq.getName(),
+ AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ currentSeq.getSequenceAsString()
+ ),
+ currentSeq.getStart(),
+ currentSeq.getEnd());
+ seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
+ seqs[i].setDescription(currentSeq.getDescription());
+ getSequenceAt(i).setSequenceFeatures(null);
+ 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++;
+
+ int cLength;
+ for (int i = 0; i < sequences.size();
+ i++)
+ {
+ current = getSequenceAt(i);
+ cLength = current.getLength();
+
+ if (cLength < maxLength)
+ {
+ current.insertCharAt(cLength,
+ maxLength-cLength, 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.elementAt(i));
+ }
+ CigarArray cal = new CigarArray(alseqs);
+ cal.addOperation(CigarArray.M, getWidth());
+ return cal;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff