-/*\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 MCview.*;\r
-\r
-import jalview.analysis.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-public class Sequence implements SequenceI {\r
- protected String name;\r
- protected String sequence;\r
- protected String description;\r
- protected int start;\r
- protected int end;\r
- protected String displayId;\r
- protected Color color = Color.white;\r
- String pdbId;\r
- public Vector sequenceFeatures = new Vector();\r
-\r
- public Sequence(String name, String sequence, int start, int end) {\r
- this.name = name;\r
- this.sequence = sequence;\r
- this.start = start;\r
- this.end = end;\r
-\r
- setDisplayId();\r
- }\r
-\r
- public Sequence(String name, String sequence) {\r
- this(name, sequence, 1, sequence.length());\r
- }\r
-\r
- public Sequence(SequenceI seq) {\r
- this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());\r
- }\r
-\r
- public void setSequenceFeatures(Vector v) {\r
- sequenceFeatures = v;\r
- }\r
-\r
- public Vector getSequenceFeatures() {\r
- return sequenceFeatures;\r
- }\r
-\r
- public void setPDBId(String id) {\r
- pdbId = id;\r
- }\r
-\r
- public String getPDBId() {\r
- return pdbId;\r
- }\r
-\r
- public String getDisplayId() {\r
- return displayId;\r
- }\r
-\r
- public void setDisplayId() {\r
- displayId = name + "/" + start + "-" + end;\r
- }\r
-\r
- public void setName(String name) {\r
- this.name = name;\r
- setDisplayId();\r
- }\r
-\r
- public String getName() {\r
- return this.name;\r
- }\r
-\r
- public void setStart(int start) {\r
- this.start = start;\r
- setDisplayId();\r
- }\r
-\r
- public int getStart() {\r
- return this.start;\r
- }\r
-\r
- public void setEnd(int end) {\r
- this.end = end;\r
- setDisplayId();\r
- }\r
-\r
- public int getEnd() {\r
- return this.end;\r
- }\r
-\r
- public int getLength() {\r
- return this.sequence.length();\r
- }\r
-\r
- public void setSequence(String seq) {\r
- this.sequence = seq;\r
- }\r
-\r
- public String getSequence() {\r
- return this.sequence;\r
- }\r
-\r
- public String getSequence(int start, int end) {\r
- // JBPNote - left to user to pad the result here (TODO:Decide on this policy)\r
- if (start >= sequence.length()) {\r
- return "";\r
- }\r
-\r
- if (end >= sequence.length()) {\r
- end = sequence.length();\r
- }\r
-\r
- return this.sequence.substring(start, end);\r
- }\r
-\r
- public char getCharAt(int i) {\r
- if (i < sequence.length()) {\r
- return sequence.charAt(i);\r
- } else {\r
- return ' ';\r
- }\r
- }\r
-\r
- public void setDescription(String desc) {\r
- this.description = desc;\r
- }\r
-\r
- public String getDescription() {\r
- return this.description;\r
- }\r
-\r
- public int findIndex(int pos) {\r
- // returns the alignment position for a residue\r
- int j = start;\r
- int i = 0;\r
-\r
- while ((i < sequence.length()) && (j <= end) && (j <= pos)) {\r
- char c = sequence.charAt(i);\r
-\r
- if (!jalview.util.Comparison.isGap((c))) {\r
- j++;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- if ((j == end) && (j < pos)) {\r
- return end + 1;\r
- } else {\r
- return i;\r
- }\r
- }\r
-\r
- public int findPosition(int i) {\r
- // Returns the sequence position for an alignment position\r
- int j = 0;\r
- int pos = start;\r
-\r
- while ((j < i) && (j < sequence.length())) {\r
- char c = sequence.charAt(j);\r
-\r
- if (!jalview.util.Comparison.isGap((c))) {\r
- pos++;\r
- }\r
-\r
- j++;\r
- }\r
-\r
- return pos;\r
- }\r
-\r
- public int[] gapMap() {\r
- // Returns an int array giving the position of each residue in the sequence in the alignment\r
- String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);\r
- int[] map = new int[seq.length()];\r
- int j = 0;\r
- int p = 0;\r
-\r
- while (j < sequence.length()) {\r
- if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {\r
- map[p++] = j;\r
- }\r
-\r
- j++;\r
- }\r
-\r
- return map;\r
- }\r
-\r
- public void deleteCharAt(int i) {\r
- if (i >= sequence.length()) {\r
- return;\r
- }\r
-\r
- sequence = sequence.substring(0, i) + sequence.substring(i + 1);\r
- }\r
-\r
- public void deleteChars(int i, int j) {\r
- if (i >= sequence.length()) {\r
- return;\r
- }\r
-\r
- if (j >= sequence.length()) {\r
- sequence = sequence.substring(0, i);\r
- } else {\r
- sequence = sequence.substring(0, i) + sequence.substring(j);\r
- }\r
- }\r
-\r
- public void insertCharAt(int i, char c) {\r
- insertCharAt(i, c, true);\r
- }\r
-\r
- public void insertCharAt(int i, char c, boolean chop) {\r
- String tmp = new String(sequence);\r
-\r
- if (i < sequence.length()) {\r
- sequence = tmp.substring(0, i) + String.valueOf(c) +\r
- tmp.substring(i);\r
- } else {\r
- // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!\r
- char[] ch = new char[(1 + i) - sequence.length()];\r
-\r
- for (int j = 0, k = ch.length; j < k; j++)\r
- ch[j] = c;\r
-\r
- sequence = tmp + String.valueOf(ch);\r
- }\r
- }\r
-\r
- public void setColor(Color c) {\r
- this.color = c;\r
- }\r
-\r
- public Color getColor() {\r
- return color;\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 java.awt.*;
+
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Sequence implements SequenceI
+{
+ SequenceI datasetSequence;
+ String name;
+ private String sequence;
+ String description;
+ int start;
+ int end;
+ Vector pdbIds;
+ String vamsasId;
+ DBRefEntry[] dbrefs;
+
+ /** This annotation is displayed below the alignment but the
+ * positions are tied to the residues of this sequence */
+ Vector annotation;
+
+ /** DOCUMENT ME!! */
+ public SequenceFeature[] sequenceFeatures;
+
+ /** This array holds hidden sequences
+ * of which this sequence is the representitive member of a group
+ */
+ SequenceGroup hiddenSequences;
+
+ /**
+ * Creates a new Sequence object.
+ *
+ * @param name DOCUMENT ME!
+ * @param sequence DOCUMENT ME!
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ */
+ public Sequence(String name, String sequence, int start, int end)
+ {
+ this.name = name;
+ this.sequence = sequence;
+ this.start = start;
+ this.end = end;
+
+ parseId();
+
+ checkValidRange();
+ }
+
+ com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
+ "[/][0-9]{1,}[-][0-9]{1,}$");
+ com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
+ "[0-9]{1,}$");
+
+ void parseId()
+ {
+ // Does sequence have the /start-end signiature?
+ if (limitrx.search(name))
+ {
+ name = limitrx.left();
+ endrx.search(limitrx.stringMatched());
+ setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
+ endrx.matchedFrom() - 1)));
+ setEnd(Integer.parseInt(endrx.stringMatched()));
+ }
+ }
+
+ void checkValidRange()
+ {
+ if (end < 1)
+ {
+ int endRes = 0;
+ char ch;
+ for (int j = 0; j < sequence.length(); j++)
+ {
+ ch = sequence.charAt(j);
+ if (!jalview.util.Comparison.isGap( (ch)))
+ {
+ endRes++;
+ }
+ }
+ if (endRes > 0)
+ {
+ endRes += start - 1;
+ }
+
+ this.end = endRes;
+ }
+
+ }
+
+ /**
+ * Creates a new Sequence object.
+ *
+ * @param name DOCUMENT ME!
+ * @param sequence DOCUMENT ME!
+ */
+ public Sequence(String name, String sequence)
+ {
+ this(name, sequence, 1, -1);
+ }
+
+ /**
+ * Creates a new Sequence object.
+ *
+ * @param seq DOCUMENT ME!
+ */
+ public Sequence(SequenceI seq)
+ {
+ this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v DOCUMENT ME!
+ */
+ public void setSequenceFeatures(SequenceFeature[] features)
+ {
+ sequenceFeatures = features;
+ }
+
+ public synchronized void addSequenceFeature(SequenceFeature sf)
+ {
+ if (sequenceFeatures == null)
+ {
+ sequenceFeatures = new SequenceFeature[0];
+ }
+
+ for (int i = 0; i < sequenceFeatures.length; i++)
+ {
+ if (sequenceFeatures[i].equals(sf))
+ {
+ return;
+ }
+ }
+
+ SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
+ System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
+ temp[sequenceFeatures.length] = sf;
+
+ sequenceFeatures = temp;
+ }
+
+ public void deleteFeature(SequenceFeature sf)
+ {
+ if(sequenceFeatures==null)
+ return;
+
+ int index=0;
+ for (index = 0; index < sequenceFeatures.length; index++)
+ {
+ if (sequenceFeatures[index].equals(sf))
+ {
+ break;
+ }
+ }
+
+
+ if(index==sequenceFeatures.length)
+ return;
+
+ int sfLength = sequenceFeatures.length;
+ if(sfLength<2)
+ {
+ sequenceFeatures = null;
+ }
+ else
+ {
+ SequenceFeature[] temp = new SequenceFeature[sfLength-1];
+ System.arraycopy(sequenceFeatures, 0, temp, 0, index);
+
+ if(index<sfLength)
+ System.arraycopy(sequenceFeatures,
+ index + 1,
+ temp,
+ index, sequenceFeatures.length - index -1);
+
+ sequenceFeatures = temp;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceFeature[] getSequenceFeatures()
+ {
+ return sequenceFeatures;
+ }
+
+ public void addPDBId(PDBEntry entry)
+ {
+ if (pdbIds == null)
+ pdbIds = new Vector();
+
+ pdbIds.addElement(entry);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ */
+ public void setPDBId(Vector id)
+ {
+ pdbIds = id;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getPDBId()
+ {
+ return pdbIds;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDisplayId(boolean jvsuffix)
+ {
+ StringBuffer result = new StringBuffer(name);
+ if (jvsuffix)
+ {
+ result.append("/" + start + "-" + end);
+ }
+
+ return result.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setName(String name)
+ {
+ this.name = name;
+ this.parseId();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName()
+ {
+ return this.name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start DOCUMENT ME!
+ */
+ public void setStart(int start)
+ {
+ this.start = start;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStart()
+ {
+ return this.start;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param end DOCUMENT ME!
+ */
+ public void setEnd(int end)
+ {
+ this.end = end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEnd()
+ {
+ return this.end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getLength()
+ {
+ return this.sequence.length();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ */
+ public void setSequence(String seq)
+ {
+ this.sequence = seq;
+ checkValidRange();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSequence()
+ {
+ return this.sequence;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSequence(int start, int end)
+ {
+ // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
+ if (start >= sequence.length())
+ {
+ return "";
+ }
+
+ if (end >= sequence.length())
+ {
+ end = sequence.length();
+ }
+
+ return this.sequence.substring(start, end);
+ }
+
+ /**
+ * make a new Sequence object from start to end (including gaps) over this seqeunce
+ * @param start int
+ * @param end int
+ * @return SequenceI
+ */
+ public SequenceI getSubSequence(int start, int end)
+ {
+ if (start < 0)
+ start = 0;
+ String seq = getSequence(start, end);
+ if (seq == "")
+ return null;
+ int nstart = findPosition(start);
+ int nend = findPosition(end) - 1;
+ // JBPNote - this is an incomplete copy.
+ SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
+ nseq.setDescription(description);
+ nseq.setDatasetSequence(getDatasetSequence());
+ return nseq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getCharAt(int i)
+ {
+ if (i < sequence.length())
+ {
+ return sequence.charAt(i);
+ }
+ else
+ {
+ return ' ';
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void setDescription(String desc)
+ {
+ this.description = desc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription()
+ {
+ return this.description;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pos DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int findIndex(int pos)
+ {
+ // returns the alignment position for a residue
+ int j = start;
+ int i = 0;
+
+ while ( (i < sequence.length()) && (j <= end) && (j <= pos))
+ {
+ if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
+ {
+ j++;
+ }
+
+ i++;
+ }
+
+ if ( (j == end) && (j < pos))
+ {
+ return end + 1;
+ }
+ else
+ {
+ return i;
+ }
+ }
+
+ /**
+ * Returns the sequence position for an alignment position
+ *
+ * @param i column index in alignment (from 1)
+ *
+ * @return residue number for residue (left of and) nearest ith column
+ */
+ public int findPosition(int i)
+ {
+ int j = 0;
+ int pos = start;
+ int seqlen = sequence.length();
+ while ( (j < i) && (j < seqlen))
+ {
+ if (!jalview.util.Comparison.isGap( (sequence.charAt(j))))
+ {
+ pos++;
+ }
+
+ j++;
+ }
+
+ return pos;
+ }
+
+ /**
+ * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
+ *
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
+ */
+ public int[] gapMap()
+ {
+ String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.
+ GapChars, sequence);
+ int[] map = new int[seq.length()];
+ int j = 0;
+ int p = 0;
+
+ while (j < sequence.length())
+ {
+ if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
+ {
+ map[p++] = j;
+ }
+
+ j++;
+ }
+
+ return map;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ */
+ public void deleteCharAt(int i)
+ {
+ if (i >= sequence.length())
+ {
+ return;
+ }
+
+ sequence = sequence.substring(0, i) + sequence.substring(i + 1);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param j DOCUMENT ME!
+ */
+ public void deleteChars(int i, int j)
+ {
+ if (i >= sequence.length())
+ {
+ return;
+ }
+
+ if (j >= sequence.length())
+ {
+ sequence = sequence.substring(0, i);
+ }
+ else
+ {
+ sequence = sequence.substring(0, i) + sequence.substring(j);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param c DOCUMENT ME!
+ * @param chop DOCUMENT ME!
+ */
+ public void insertCharAt(int i, int length, char c)
+ {
+ StringBuffer tmp;
+
+ if (i >= sequence.length())
+ {
+ tmp = new StringBuffer(sequence);
+ }
+ else
+ tmp = new StringBuffer(sequence.substring(0, i));
+
+ while (length > 0)
+ {
+ tmp.append(c);
+ length--;
+ }
+
+ if (i < sequence.length())
+ {
+ tmp.append(sequence.substring(i));
+ }
+
+ sequence = tmp.toString();
+ }
+
+ public void insertCharAt(int i, char c)
+ {
+ insertCharAt(i, 1, c);
+ }
+
+ public String getVamsasId()
+ {
+ return vamsasId;
+ }
+
+ public void setVamsasId(String id)
+ {
+ vamsasId = id;
+ }
+
+ public void setDBRef(DBRefEntry[] dbref)
+ {
+ dbrefs = dbref;
+ }
+
+ public DBRefEntry[] getDBRef()
+ {
+ return dbrefs;
+ }
+
+ public void addDBRef(DBRefEntry entry)
+ {
+ if (dbrefs == null)
+ dbrefs = new DBRefEntry[0];
+
+ DBRefEntry[] temp = new DBRefEntry[dbrefs.length + 1];
+ System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
+
+ temp[temp.length - 1] = entry;
+
+ dbrefs = temp;
+ }
+
+ public void setDatasetSequence(SequenceI seq)
+ {
+ datasetSequence = seq;
+ }
+
+ public SequenceI getDatasetSequence()
+ {
+ return datasetSequence;
+ }
+
+ public AlignmentAnnotation[] getAnnotation()
+ {
+ if (annotation == null)
+ return null;
+
+ AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
+ for (int r = 0; r < ret.length; r++)
+ ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
+
+ return ret;
+ }
+
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+ {
+ if (this.annotation == null)
+ this.annotation = new Vector();
+
+ this.annotation.addElement(annotation);
+ }
+
+ public SequenceGroup getHiddenSequences()
+ {
+ return hiddenSequences;
+ }
+
+ public void addHiddenSequence(SequenceI seq)
+ {
+ if (hiddenSequences == null)
+ {
+ hiddenSequences = new SequenceGroup();
+ }
+ hiddenSequences.addSequence(seq, false);
+ }
+
+ public void showHiddenSequence(SequenceI seq)
+ {
+ hiddenSequences.deleteSequence(seq, false);
+ if (hiddenSequences.getSize(false) < 1)
+ {
+ hiddenSequences = null;
+ }
+ }
+}
+
+
git://source.jalview.org / jalview.git / blobdiff