+/*\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
import java.awt.*;\r
-import java.util.StringTokenizer;\r
-import MCview.*;\r
\r
+import java.util.*;\r
\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class Sequence implements SequenceI\r
{\r
- protected String name;\r
- protected String sequence;\r
- protected int start;\r
- protected int end;\r
- protected String description;\r
- protected int charHeight;\r
- protected String displayId;\r
- protected Color color = Color.white;\r
- PDBfile pdb;\r
- public int maxchain = -1;\r
-\r
- public int pdbstart;\r
- public int pdbend;\r
- public int seqstart;\r
- public int seqend;\r
- public void setPDBfile(PDBfile pdb)\r
- {\r
- this.pdb = pdb;\r
- int max = -10;\r
- maxchain = -1;\r
-\r
- for (int i=0; i < pdb.chains.size(); i++) {\r
-\r
- System.out.println("PDB sequence = " + ((PDBChain)pdb.chains.elementAt(i)).sequence);\r
- // Now lets compare the sequences to get\r
- // the start and end points.\r
-\r
-\r
- StringTokenizer str = new StringTokenizer(sequence, ".");\r
- String newString = "";\r
-\r
- while (str.hasMoreTokens()) {\r
- newString += str.nextToken();\r
- }\r
- // Align the sequence to the pdb\r
- AlignSeq as = new AlignSeq(this,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\r
-\r
- System.out.println("Score = " + as.maxscore);\r
- if (as.maxscore > max) {\r
- System.out.println("New max score");\r
- max = as.maxscore;\r
- maxchain = i;\r
-\r
- pdbstart = as.seq2start;\r
- pdbend = as.seq2end;\r
- seqstart = as.seq1start - 1 ;\r
- seqend = as.seq1end -1;\r
- }\r
-\r
- System.out.println("PDB start/end " + pdbstart + " " + pdbend);\r
- System.out.println("SEQ start/end " + seqstart + " " + seqend);\r
- }\r
- }\r
-\r
- public Sequence(String name, String sequence, int start, int end)\r
- {\r
-\r
- this.name = name;\r
- this.sequence = sequence;\r
- this.start = start;\r
- this.end = end;\r
-\r
- setDisplayId();\r
-\r
- }\r
-\r
- public Sequence(String name,String sequence) {\r
- this(name,sequence,1,sequence.length());\r
- }\r
- public Sequence(SequenceI seq) {\r
- this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());\r
- }\r
- public String getDisplayId() {\r
- return displayId;\r
- }\r
- public void setDisplayId() {\r
- displayId = name + "/" + start + "-" + end;\r
- }\r
- public void setName(String name) {\r
- this.name = name;\r
- setDisplayId();\r
- }\r
- public String getName() {\r
- return this.name;\r
- }\r
- public void setStart(int start) {\r
- this.start = start;\r
- setDisplayId();\r
- }\r
- public int getStart() {\r
- return this.start;\r
- }\r
- public void setEnd(int end) {\r
- this.end = end;\r
- setDisplayId();\r
- }\r
- public int getEnd() {\r
- return this.end;\r
- }\r
- public int getLength() {\r
- return this.sequence.length();\r
- }\r
- public void setSequence(String seq) {\r
- this.sequence = seq;\r
- }\r
- public String getSequence() {\r
- return this.sequence;\r
- }\r
- public String getSequence(int start,int end) {\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
- public void setDescription(String desc) {\r
- this.description = desc;\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
-\r
- String s = sequence.substring(i,i+1);\r
-\r
- if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {\r
- j++;\r
+ SequenceI datasetSequence;\r
+ String name;\r
+ String shortName;\r
+ String sequence;\r
+ String description;\r
+ int start;\r
+ int end;\r
+ Color color = Color.white;\r
+ Vector pdbIds;\r
+ String vamsasId;\r
+ Vector dbrefs;\r
+\r
+\r
+ /** DOCUMENT ME!! */\r
+ public Vector sequenceFeatures = new Vector();\r
+\r
+ /**\r
+ * Creates a new Sequence object.\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ * @param sequence DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public Sequence(String name, String sequence, int start, int end)\r
+ {\r
+ this.name = name;\r
+ parseId();\r
+\r
+ this.sequence = sequence;\r
+ this.start = start;\r
+ this.end = end;\r
+\r
+ checkValidRange();\r
+ }\r
+\r
+ void parseId()\r
+ {\r
+ // Read in any DB refs first\r
+ StringTokenizer st = new StringTokenizer(name, "|");\r
+ if(st.countTokens()<1)\r
+ {\r
+ shortName = name;\r
+ return;\r
+ }\r
+\r
+ while (st.countTokens() > 1)\r
+ {\r
+ String a = st.nextToken();\r
+ String b = st.nextToken();\r
+ addDBRef(new DBRefEntry(a, "0", b));\r
+ }\r
+\r
+ if (st.hasMoreTokens())\r
+ shortName = st.nextToken();\r
+\r
+ // Remove /start-end from sequence\r
+ if (shortName.indexOf("/") > 0)\r
+ {\r
+ st = new StringTokenizer(shortName, "/");\r
+ String limits = null;\r
+ try\r
+ {\r
+ if (st.countTokens() == 2)\r
+ {\r
+\r
+ shortName = st.nextToken();\r
+\r
+ limits = st.nextToken();\r
+\r
+ st = new StringTokenizer(limits, "-");\r
+\r
+ if (st.countTokens() == 2)\r
+ {\r
+ setStart(Integer.valueOf(st.nextToken()).intValue());\r
+ setEnd(Integer.valueOf(st.nextToken()).intValue());\r
+ }\r
+ }\r
+\r
+ // If we're still in this loop, parsing of start and end was ok\r
+ // Therefore remove it from the sequence name\r
+ name = name.substring(0, name.indexOf("/"));\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {\r
+ // Problem parsing sequence limits. Just add it back to the\r
+ // Id so we dont lose this info\r
+ shortName += "/" + limits;\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ void checkValidRange()\r
+ {\r
+ if (end < 1)\r
+ {\r
+ int endRes = 0;\r
+ char ch;\r
+ for (int j = 0; j < sequence.length(); j++)\r
+ {\r
+ ch = sequence.charAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ endRes++;\r
+ }\r
+ }\r
+ if (endRes > 0)\r
+ {\r
+ endRes += start - 1;\r
+ }\r
+\r
+ this.end = endRes;\r
}\r
- i++;\r
+\r
+ }\r
+\r
+ /**\r
+ * Creates a new Sequence object.\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ * @param sequence DOCUMENT ME!\r
+ */\r
+ public Sequence(String name, String sequence)\r
+ {\r
+ this(name, sequence, 1, -1);\r
+ }\r
+\r
+ /**\r
+ * Creates a new Sequence object.\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ public Sequence(SequenceI seq)\r
+ {\r
+ this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param v DOCUMENT ME!\r
+ */\r
+ public void setSequenceFeatures(Vector v)\r
+ {\r
+ sequenceFeatures = v;\r
+ }\r
+\r
+ public void addSequenceFeature(SequenceFeature sf)\r
+ {\r
+ if(sequenceFeatures==null)\r
+ sequenceFeatures = new Vector();\r
+\r
+ sequenceFeatures.addElement(sf);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getSequenceFeatures()\r
+ {\r
+ return sequenceFeatures;\r
}\r
- if (j == end && j < pos) {\r
- return end+1;\r
- } else {\r
\r
- return i;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param id DOCUMENT ME!\r
+ */\r
+ public void setPDBId(Vector id)\r
+ {\r
+ pdbIds = id;\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
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getPDBId()\r
+ {\r
+ return pdbIds;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDisplayId(boolean dbref, boolean jvsuffix)\r
+ {\r
+ StringBuffer result = new StringBuffer();\r
+ if (dbref && dbrefs != null)\r
+ {\r
+ for (int i = 0; i < dbrefs.size(); i++)\r
+ {\r
+ DBRefEntry entry = (DBRefEntry) dbrefs.elementAt(i);\r
+ result.append(entry.getSource() + "|" + entry.getAccessionId() + "|");\r
+ }\r
+ }\r
\r
- while (j < i) {\r
- String s = sequence.substring(j,j+1);\r
+ result.append(shortName);\r
\r
- if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {\r
- pos++;\r
+ if (jvsuffix)\r
+ {\r
+ result.append("/" + start + "-" + end);\r
}\r
- j++;\r
+\r
+ return result.toString();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ */\r
+ public void setName(String name)\r
+ {\r
+ this.name = name;\r
+ this.parseId();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName()\r
+ {\r
+ return this.name;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param start DOCUMENT ME!\r
+ */\r
+ public void setStart(int start)\r
+ {\r
+ this.start = start;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getStart()\r
+ {\r
+ return this.start;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public void setEnd(int end)\r
+ {\r
+ this.end = end;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getEnd()\r
+ {\r
+ return this.end;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getLength()\r
+ {\r
+ return this.sequence.length();\r
}\r
- return pos;\r
- }\r
- public void deleteCharAt(int i)\r
- {\r
- StringBuffer sbuffer = new StringBuffer(sequence);\r
- sbuffer.deleteCharAt(i);\r
- sequence = sbuffer.toString();\r
- }\r
\r
- public void insertCharAt(int i, char c)\r
- {\r
- insertCharAt(i,c,true);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ public void setSequence(String seq)\r
+ {\r
+ this.sequence = seq;\r
+ checkValidRange();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getSequence()\r
+ {\r
+ return this.sequence;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getSequence(int start, int end)\r
+ {\r
+ // JBPNote - left to user to pad the result here (TODO:Decide on this policy)\r
+ if (start >= sequence.length())\r
+ {\r
+ return "";\r
+ }\r
+\r
+ if (end >= sequence.length())\r
+ {\r
+ end = sequence.length();\r
+ }\r
+\r
+ return this.sequence.substring(start, end);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public char getCharAt(int i)\r
+ {\r
+ if (i < sequence.length())\r
+ {\r
+ return sequence.charAt(i);\r
+ }\r
+ else\r
+ {\r
+ return ' ';\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param desc DOCUMENT ME!\r
+ */\r
+ public void setDescription(String desc)\r
+ {\r
+ this.description = desc;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDescription()\r
+ {\r
+ return this.description;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pos DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int findIndex(int pos)\r
+ {\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
+ {\r
+ char c = sequence.charAt(i);\r
+\r
+ if (!jalview.util.Comparison.isGap((c)))\r
+ {\r
+ j++;\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ if ((j == end) && (j < pos))\r
+ {\r
+ return end + 1;\r
+ }\r
+ else\r
+ {\r
+ return i;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int findPosition(int i)\r
+ {\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
+ {\r
+ char c = sequence.charAt(j);\r
+\r
+ if (!jalview.util.Comparison.isGap((c)))\r
+ {\r
+ pos++;\r
+ }\r
+\r
+ j++;\r
+ }\r
+\r
+ return pos;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int[] gapMap()\r
+ {\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
+ {\r
+ if (!jalview.util.Comparison.isGap(sequence.charAt(j)))\r
+ {\r
+ map[p++] = j;\r
+ }\r
+\r
+ j++;\r
+ }\r
+\r
+ return map;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
+ public void deleteCharAt(int i)\r
+ {\r
+ if (i >= sequence.length())\r
+ {\r
+ return;\r
+ }\r
+\r
+ sequence = sequence.substring(0, i) + sequence.substring(i + 1);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param j DOCUMENT ME!\r
+ */\r
+ public void deleteChars(int i, int j)\r
+ {\r
+ if (i >= sequence.length())\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (j >= sequence.length())\r
+ {\r
+ sequence = sequence.substring(0, i);\r
+ }\r
+ else\r
+ {\r
+ sequence = sequence.substring(0, i) + sequence.substring(j);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param c DOCUMENT ME!\r
+ */\r
+ public void insertCharAt(int i, char c)\r
+ {\r
+ insertCharAt(i, c, true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param c DOCUMENT ME!\r
+ * @param chop DOCUMENT ME!\r
+ */\r
+ public void insertCharAt(int i, char c, boolean chop)\r
+ {\r
+ String tmp = new String(sequence);\r
+\r
+ if (i < sequence.length())\r
+ {\r
+ sequence = tmp.substring(0, i) + String.valueOf(c) +\r
+ tmp.substring(i);\r
+ }\r
+ else\r
+ {\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ */\r
+ public void setColor(Color c)\r
+ {\r
+ this.color = c;\r
+ }\r
\r
- public void insertCharAt(int i,char c,boolean chop) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Color getColor()\r
+ {\r
+ return color;\r
+ }\r
\r
- String tmp = new String(sequence);\r
+ public String getVamsasId()\r
+ {\r
+ return vamsasId;\r
+ }\r
\r
- if (i < sequence.length()) {\r
- sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);\r
- } else {\r
- sequence = tmp + String.valueOf(c);\r
+ public void setVamsasId(String id)\r
+ {\r
+ vamsasId = id;\r
}\r
\r
- }\r
+ public void setDBRef(Vector dbref)\r
+ {\r
+ dbrefs = dbref;\r
+ }\r
+ public Vector getDBRef()\r
+ {\r
+ return dbrefs;\r
+ }\r
\r
- public void setColor(Color c) {\r
- this.color = c;\r
- }\r
+ public void addDBRef(DBRefEntry entry)\r
+ {\r
+ if(dbrefs == null)\r
+ dbrefs = new Vector();\r
\r
- public Color getColor() {\r
- return color;\r
- }\r
+ dbrefs.addElement(entry);\r
+ }\r
+\r
+ public void setDatasetSequence(SequenceI seq)\r
+ {\r
+ datasetSequence = seq;\r
+ }\r
+\r
+ public SequenceI getDatasetSequence()\r
+ {\r
+ return datasetSequence;\r
+ }\r
\r
}\r