\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 Alignment dataset;\r
protected Vector sequences;\r
protected Vector groups = new Vector();\r
- protected Vector superGroup = new Vector();\r
protected char gapCharacter = '-';\r
protected int type = NUCLEOTIDE;\r
public static final int PROTEIN = 0;\r
/** DOCUMENT ME!! */\r
public AlignmentAnnotation[] annotations;\r
\r
+ HiddenSequences hiddenSequences = new HiddenSequences(this);\r
+\r
+\r
/** Make an alignment from an array of Sequences.\r
*\r
* @param sequences\r
{\r
sequences.addElement(seqs[i]);\r
}\r
-\r
- getWidth();\r
}\r
\r
/**\r
return sequences;\r
}\r
\r
+ public SequenceI [] getSequencesArray()\r
+ {\r
+ SequenceI [] reply = new SequenceI[sequences.size()];\r
+ for(int i=0; i<sequences.size(); i++)\r
+ {\r
+ reply[i] = (SequenceI)sequences.elementAt(i);\r
+ }\r
+ return reply;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public void addSequence(SequenceI snew)\r
{\r
- sequences.addElement(snew);\r
- }\r
+ if(dataset!=null)\r
+ {\r
+ Sequence ds = new Sequence(snew.getName(),\r
+ AlignSeq.extractGaps("-. ", snew.getSequence()),\r
+ snew.getStart(),\r
+ snew.getEnd());\r
\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
+ snew.setDatasetSequence(ds);\r
+ getDataset().addSequence(ds);\r
+ }\r
+\r
+ sequences.addElement(snew);\r
}\r
\r
+\r
/** Adds a sequence to the alignment. Recalculates maxLength and size.\r
*\r
* @param snew\r
sequences.removeElementAt(i);\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
- 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
- // Now delete the sequences\r
- for (int i = 0; i < del.size(); i++)\r
- {\r
- deleteSequence((SequenceI) del.elementAt(i));\r
- }\r
-\r
- return del;\r
- }\r
-\r
- /** */\r
- public SequenceGroup findGroup(int i)\r
- {\r
- return findGroup(getSequenceAt(i));\r
- }\r
\r
/** */\r
public SequenceGroup findGroup(SequenceI s)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
- if (sg.sequences.contains(s))\r
+ if (sg.getSequences(false).contains(s))\r
{\r
return sg;\r
}\r
for (int i = 0; i < gSize; i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if(sg==null || sg.sequences==null)\r
+ if(sg==null || sg.getSequences(false)==null)\r
{\r
this.deleteGroup(sg);\r
gSize--;\r
continue;\r
}\r
\r
- if (sg.sequences.contains(s))\r
+ if (sg.getSequences(false).contains(s))\r
{\r
temp.addElement(sg);\r
}\r
return ret;\r
}\r
\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
- /**\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
- * 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
- if (temp.sequenceGroups.contains(sg))\r
- {\r
- return temp;\r
- }\r
- }\r
-\r
- return null;\r
- }\r
\r
/** */\r
public void addGroup(SequenceGroup sg)\r
public void deleteAllGroups()\r
{\r
groups.removeAllElements();\r
- superGroup.removeAllElements();\r
\r
int i = 0;\r
\r
}\r
\r
\r
- public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index)\r
+ public void adjustSequenceAnnotations()\r
{\r
- aa.refSequence = seqRef;\r
- if(seqRef!=null && index!=0)\r
+ if(annotations!=null)\r
{\r
- int aSize = aa.annotations.length;\r
- int newIndex;\r
- Annotation [] temp = new Annotation[seqRef.getLength()];\r
- for(int a=0; a<aSize; a++)\r
+ for (int a = 0; a < annotations.length; a++)\r
{\r
- newIndex = seqRef.findIndex(a + index)-1;\r
- temp[newIndex] = aa.annotations[a];\r
+ if (annotations[a].sequenceRef != null)\r
+ {\r
+ annotations[a].adjustForAlignment();\r
+ }\r
}\r
-\r
- aa.annotations = temp;\r
}\r
-\r
- addAnnotation(aa);\r
}\r
\r
/**\r
public void addAnnotation(AlignmentAnnotation aa)\r
{\r
int aSize = 1;\r
-\r
if (annotations != null)\r
{\r
aSize = annotations.length + 1;\r
}\r
\r
-\r
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
\r
- temp[0] = aa;\r
+ temp[aSize-1] = aa;\r
\r
- int i = 1;\r
+ int i = 0;\r
\r
if (aSize > 1)\r
{\r
- for (i = 1; i < (aSize); i++)\r
+ for (i = 0; i < (aSize-1); i++)\r
{\r
- temp[i] = annotations[i-1];\r
+ temp[i] = annotations[i];\r
}\r
}\r
\r
annotations = temp;\r
}\r
\r
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index)\r
+ {\r
+ if(aa==null || annotations==null || annotations.length-1<index)\r
+ return;\r
+\r
+ int aSize = annotations.length;\r
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
+\r
+ temp[index] = aa;\r
+\r
+ for (int i = 0; i < aSize; i++)\r
+ {\r
+ if(i==index)\r
+ continue;\r
+\r
+ if(i<index)\r
+ temp[i] = annotations[i];\r
+ else\r
+ temp[i] = annotations[i-1];\r
+ }\r
+\r
+ annotations = temp;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
\r
public boolean padGaps() {\r
boolean modified=false;\r
- int Width = getWidth();\r
+\r
+ //Remove excess gaps from the end of alignment\r
+ int maxLength = -1;\r
+\r
SequenceI current;\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ current = getSequenceAt(i);\r
+ for (int j = current.getLength(); j > maxLength; j--)\r
+ {\r
+ if (j > maxLength && !jalview.util.Comparison.isGap(\r
+ current.getCharAt(j)))\r
+ {\r
+ maxLength = j;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ maxLength++;\r
+\r
for (int i = 0; i < sequences.size();\r
i++)\r
{\r
current = getSequenceAt(i);\r
\r
- if (current.getLength() < Width)\r
+ if (current.getLength() < maxLength)\r
{\r
- current.insertCharAt(Width - 1, gapCharacter);\r
+ current.insertCharAt(maxLength - 1, gapCharacter);\r
modified=true;\r
}\r
+ else if(current.getLength() > maxLength)\r
+ {\r
+ current.deleteChars(maxLength, current.getLength());\r
+ }\r
}\r
return modified;\r
}\r
+\r
+ public HiddenSequences getHiddenSequences()\r
+ {\r
+ return hiddenSequences;\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff