* 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
-\r
package jalview.datamodel;\r
\r
+import MCview.*;\r
+\r
import jalview.analysis.*;\r
+\r
import java.awt.*;\r
+\r
import java.util.*;\r
-import MCview.*;\r
\r
\r
-public class Sequence implements SequenceI\r
-{\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
-\r
- public Vector sequenceFeatures = new Vector();\r
- public void setSequenceFeatures(Vector v)\r
- {\r
- sequenceFeatures = v;\r
- }\r
-\r
- public Vector getSequenceFeatures()\r
- {return sequenceFeatures; }\r
-\r
- public void setPDBId(String id)\r
- {\r
- pdbId = id;\r
- }\r
- public String getPDBId()\r
- {\r
- return pdbId;\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
- // JBPNote - left to user to pad the result here (TODO:Decide on this policy)\r
- if(start>=sequence.length())\r
- return "";\r
-\r
- if(end>=sequence.length())\r
- end = sequence.length();\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
- 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
- char c = sequence.charAt(i);\r
-\r
- if (!jalview.util.Comparison.isGap((c)))\r
- j++;\r
-\r
- i++;\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
- {\r
- char c = sequence.charAt(j);\r
- if (!jalview.util.Comparison.isGap((c)))\r
- pos++;\r
-\r
- j++;\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
- while (j<sequence.length()) {\r
- if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {\r
- map[p++]=j;\r
- }\r
- j++;\r
- }\r
- return map;\r
- }\r
-\r
- public void deleteCharAt(int i)\r
- {\r
- if (i>=sequence.length())\r
- return;\r
- sequence = sequence.substring(0,i) + sequence.substring(i+1);\r
- }\r
-\r
- public void deleteChars(int i, int j)\r
- {\r
- if (i>=sequence.length())\r
- return;\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
- public void insertCharAt(int i, char c)\r
- {\r
- insertCharAt(i,c,true);\r
- }\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
- sequence = tmp.substring(0,i) + String.valueOf(c) + 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
- for (int j=0, k=ch.length; j<k; j++)\r
- ch[j] = c;\r
- sequence = tmp + String.valueOf(ch);\r
- }\r
-\r
- }\r
-\r
- public void setColor(Color c) {\r
- this.color = c;\r
- }\r
-\r
- public Color getColor() {\r
- return color;\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
git://source.jalview.org / jalview.git / blobdiff