+/*\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 Alignment dataset;\r
+ protected Vector sequences;\r
+ protected Vector groups = new Vector();\r
+ protected Vector superGroup = new Vector();\r
+ protected char gapCharacter = '-';\r
+ protected Provenance provenance;\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
+ /** 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
+ int i=0;\r
\r
- protected Vector sequences;\r
- protected Vector groups = new Vector();\r
- public Hashtable[] cons;\r
- protected String gapCharacter = ".";\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
+ if( jalview.util.Comparison.isNucleotide(seqs))\r
+ type = NUCLEOTIDE;\r
+ else\r
+ type = PROTEIN;\r
\r
- SequenceGroup all = new SequenceGroup();\r
- all.setName("Group 1");\r
- groups.addElement(all);\r
+ sequences = new Vector();\r
\r
- int i = 0;\r
+ for (i = 0; i < seqs.length; i++)\r
+ {\r
+ sequences.addElement(seqs[i]);\r
+ }\r
\r
- while (i < seqs.length) {\r
- addToGroup(all,seqs[i]);\r
- i++;\r
+ getWidth();\r
}\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
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getSequences()\r
+ {\r
+ return sequences;\r
}\r
\r
- return null;\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
- /** Adds a sequence to the alignment. Recalculates maxLength and size.\r
- * Should put the new sequence in a sequence group!!!\r
- *\r
- * @param snew\r
- */\r
- public void addSequence(SequenceI snew) {\r
- sequences.addElement(snew);\r
+ return null;\r
+ }\r
\r
- ((SequenceGroup)groups.lastElement()).addSequence(snew);\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
- public void addSequence(SequenceI[] seq) {\r
- for (int i=0; i < seq.length; i++) {\r
- addSequence(seq[i]);\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
\r
- /** Adds a sequence to the alignment. Recalculates maxLength and size.\r
- * Should put the new sequence in a sequence group!!!\r
- *\r
- * @param snew\r
- */\r
- public void setSequenceAt(int i,SequenceI snew) {\r
- SequenceI oldseq = getSequenceAt(i);\r
- deleteSequence(oldseq);\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
+ sequences.setElementAt(snew, i);\r
+ }\r
\r
- ((SequenceGroup)groups.lastElement()).addSequence(snew);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getGroups()\r
+ {\r
+ return groups;\r
+ }\r
\r
- public Vector getGroups() {\r
- return groups;\r
- }\r
+ /** Takes out columns consisting entirely of gaps (-,.," ")\r
+ */\r
+ public void removeGaps()\r
+ {\r
+ SequenceI current;\r
+ int iSize = getWidth();\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
+ 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
- for (int i=0; i < groups.size(); i++) {\r
- arr[i] = ((SequenceGroup)groups.elementAt(i)).sequences.size();\r
- s[i] = groups.elementAt(i);\r
+ if (delete)\r
+ {\r
+ deleteColumns(i, i);\r
+ iSize--;\r
+ i--;\r
+ }\r
+ }\r
}\r
\r
- QuickSort.sort(arr,s);\r
-\r
- Vector newg = new Vector(groups.size());\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
- for (int i=groups.size()-1; i >= 0; i--) {\r
- newg.addElement(s[i]);\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
- groups = newg;\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
- /** Takes out columns consisting entirely of gaps (-,.," ")\r
- */\r
- public void removeGaps()\r
- {\r
+ s.setStart(newstart);\r
+ s.setSequence(s.getSequence().substring(i));\r
+ }\r
+ }\r
\r
- SequenceI current;\r
- int iSize = getWidth();\r
- for (int i=0; i < iSize; i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
+ public void trimRight(int i)\r
{\r
- boolean delete = true;\r
- for (int j=0; j < getHeight(); j++)\r
- {\r
- current = getSequenceAt(j);\r
- if (current.getLength() > i)\r
+ for (int j = 0; j < getHeight(); j++)\r
{\r
- /* MC Should move this to a method somewhere */\r
- if (current.getCharAt(i)!='-' && current.getCharAt(i)!='.' && current.getCharAt(i)!=' ')\r
- delete = false;\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
- if ( delete )\r
- {\r
- deleteColumns(i,i);\r
- iSize--;\r
- i--;\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
+ * 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
- /** 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
+ 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
- /** 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
+ // Now delete the sequences\r
+ for (int i = 0; i < del.size(); i++)\r
+ {\r
+ deleteSequence((SequenceI) del.elementAt(i));\r
+ }\r
\r
- public void deleteColumns(int seq1, int seq2, int start, int end) {\r
+ return del;\r
+ }\r
\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
+ public SequenceGroup findGroup(int i)\r
+ {\r
+ return findGroup(getSequenceAt(i));\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) + seqs[i].getSequence() + tmp.substring(pos));\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
- }\r
- }\r
+ if (sg.sequences.contains(s))\r
+ {\r
+ return sg;\r
+ }\r
+ }\r
\r
- public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {\r
- SequenceI[] seqs = new Sequence[(seq2-seq1)+1];\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
+ return null;\r
}\r
- return seqs;\r
- }\r
\r
- public void trimLeft(int i) {\r
- for (int j = 0;j< getHeight();j++) {\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
- SequenceI s = getSequenceAt(j);\r
- int newstart = s.findPosition(i);\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
- s.setStart(newstart);\r
- s.setSequence(s.getSequence().substring(i));\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
- 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
+ * DOCUMENT ME!\r
+ *\r
+ * @param sg DOCUMENT ME!\r
+ */\r
+ public void addSuperGroup(SuperGroup sg)\r
+ {\r
+ superGroup.addElement(sg);\r
+ }\r
\r
- s.setEnd(newend);\r
- s.setSequence(s.getSequence().substring(0,i+1));\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
- public void deleteSequence(SequenceI s)\r
- {\r
- for (int i=0; i < getHeight(); i++)\r
- if (getSequenceAt(i) == s)\r
- deleteSequence(i);\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
- public void deleteSequence(int i)\r
- {\r
- sequences.removeElementAt(i);\r
- }\r
+ if (temp.sequenceGroups.contains(sg))\r
+ {\r
+ return temp;\r
+ }\r
+ }\r
\r
+ return null;\r
+ }\r
\r
- public Vector removeRedundancy(float threshold, Vector sel) {\r
- Vector del = new Vector();\r
+ /** */\r
+ public void addGroup(SequenceGroup sg)\r
+ {\r
+ if (!groups.contains(sg))\r
+ {\r
+ groups.addElement(sg);\r
+ }\r
+ }\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
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void deleteAllGroups()\r
+ {\r
+ groups.removeAllElements();\r
+ superGroup.removeAllElements();\r
\r
- float pid = Comparison.compare((SequenceI)sel.elementAt(j),\r
- (SequenceI)sel.elementAt(i));\r
+ int i = 0;\r
\r
- if (pid >= threshold) {\r
- // Delete the shortest one\r
- if (((SequenceI)sel.elementAt(j)).getSequence().length() >\r
- ((SequenceI)sel.elementAt(i)).getSequence().length()) {\r
- del.addElement(sel.elementAt(i));\r
- System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());\r
- } else {\r
- del.addElement(sel.elementAt(i));\r
- System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());\r
- }\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
- // Now delete the sequences\r
- for (int i=0; i < del.size(); i++) {\r
- System.out.println("Deleting sequence " + ((SequenceI)del.elementAt(i)).getName());\r
- deleteSequence((SequenceI)del.elementAt(i));\r
+ /** */\r
+ public void deleteGroup(SequenceGroup g)\r
+ {\r
+ if (groups.contains(g))\r
+ {\r
+ groups.removeElement(g);\r
+ }\r
}\r
\r
- return del;\r
- }\r
+ /** */\r
+ public SequenceI findName(String name)\r
+ {\r
+ int i = 0;\r
\r
- public void sortByPID(SequenceI s) {\r
+ while (i < sequences.size())\r
+ {\r
+ if (getSequenceAt(i).getName().equals(name))\r
+ {\r
+ return getSequenceAt(i);\r
+ }\r
\r
- float scores[] = new float[getHeight()];\r
- SequenceI seqs[] = new SequenceI[getHeight()];\r
+ i++;\r
+ }\r
\r
- for (int i = 0; i < getHeight(); i++) {\r
- scores[i] = Comparison.compare(getSequenceAt(i),s);\r
- seqs[i] = getSequenceAt(i);\r
+ return null;\r
}\r
\r
- QuickSort.sort(scores,0,scores.length-1,seqs);\r
\r
- int len = 0;\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
- if (getHeight()%2 == 0) {\r
- len = getHeight()/2;\r
- } else {\r
- len = (getHeight()+1)/2;\r
+ return -1;\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
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getHeight()\r
+ {\r
+ return sequences.size();\r
}\r
- }\r
\r
- public void sortByID() {\r
- String ids[] = new String[getHeight()];\r
- SequenceI seqs[] = new SequenceI[getHeight()];\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
- for (int i = 0; i < getHeight(); i++) {\r
- ids[i] = getSequenceAt(i).getName();\r
- seqs[i] = getSequenceAt(i);\r
+ return maxLength;\r
}\r
\r
- QuickSort.sort(ids,seqs);\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
- int len = 0;\r
+ while (i < sequences.size())\r
+ {\r
+ SequenceI seq = getSequenceAt(i);\r
+ String tmp = seq.getName() + "/" + seq.getStart() + "-" +\r
+ seq.getEnd();\r
\r
- if (getHeight()%2 == 0) {\r
- len = getHeight()/2;\r
- } else {\r
- len = (getHeight()+1)/2;\r
- System.out.println("Sort len is odd = " + len);\r
- }\r
- for (int i = 0; i < len; i++) {\r
- System.out.println("Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName());\r
- SequenceI tmp = seqs[i];\r
- sequences.setElementAt(seqs[getHeight()-i-1],i);\r
- sequences.setElementAt(tmp,getHeight()-i-1);\r
- }\r
- }\r
+ if (tmp.length() > max)\r
+ {\r
+ max = tmp.length();\r
+ }\r
\r
- /** */\r
- public SequenceGroup findGroup(int i) {\r
- return findGroup(getSequenceAt(i));\r
- }\r
+ i++;\r
+ }\r
+\r
+ return max;\r
+ }\r
\r
- /** */\r
- public SequenceGroup findGroup(SequenceI s) {\r
- for (int i = 0; i < this.groups.size();i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param gc DOCUMENT ME!\r
+ */\r
+ public void setGapCharacter(char gc)\r
{\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
- if (sg.sequences.contains(s))\r
- return sg;\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
- return null;\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
- 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
- if (g.sequences.size() == 0) {\r
- groups.removeElement(g);\r
- }\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public char getGapCharacter()\r
+ {\r
+ return gapCharacter;\r
}\r
- }\r
-\r
- /** */\r
- public void addGroup(SequenceGroup sg) {\r
- groups.addElement(sg);\r
- }\r
-\r
- /** */\r
- public SequenceGroup addGroup() {\r
- SequenceGroup sg = new SequenceGroup();\r
- groups.addElement(sg);\r
- return sg;\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
- while (i < sequences.size()) {\r
- SequenceI s = getSequenceAt(i);\r
- if (s.getName().equals(name))\r
- return s;\r
-\r
- i++;\r
- }\r
- return null;\r
- }\r
-\r
- /** */\r
- public SequenceI findbyDisplayId(String name) {\r
- int i = 0;\r
- while (i < sequences.size()) {\r
- SequenceI s = getSequenceAt(i);\r
- if (s.getDisplayId().equals(name))\r
- return s;\r
-\r
- i++;\r
- }\r
- return null;\r
- }\r
-\r
- /** */\r
- public int findIndex(SequenceI s) {\r
- int i=0;\r
- while (i < sequences.size()) {\r
- if (s == getSequenceAt(i)) {\r
- return i;\r
- }\r
- i++;\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
- return -1;\r
- }\r
\r
- public int getHeight() {\r
- return sequences.size();\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
- public int getWidth()\r
- {\r
- int maxLength = -1;\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- if (getSequenceAt(i).getLength() > maxLength)\r
- maxLength = getSequenceAt(i).getLength();\r
+ return true;\r
}\r
\r
- return maxLength;\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
- public int getMaxIdLength() {\r
- int max = 0;\r
- int i = 0;\r
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];\r
\r
- while (i < sequences.size()) {\r
- SequenceI seq = getSequenceAt(i);\r
- String tmp = seq.getName() + "/" + seq.getStart() + "-" + seq.getEnd();\r
+ int tIndex = 0;\r
\r
- if (tmp.length() > max) {\r
- max = tmp.length();\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
- i++;\r
+ annotations = temp;\r
}\r
- return max;\r
- }\r
\r
- public void setGapCharacter(String gc) {\r
- gapCharacter = gc;\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
- public String getGapCharacter() {\r
- return gapCharacter;\r
- }\r
+ if (annotations != null)\r
+ {\r
+ aSize = annotations.length + 1;\r
+ }\r
\r
- public Vector getAAFrequency()\r
- {\r
- return AAFrequency.calculate(sequences, 0, getWidth());\r
- }\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
+ 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
+\r
+ seqs[i] = new Sequence(getSequenceAt(i).getDisplayId(true),\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
+ 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 void setProvenance(Provenance prov)\r
+ {\r
+ provenance = prov;\r
+ }\r
+ public Provenance getProvenance()\r
+ {\r
+ return provenance;\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff