\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 boolean isNucleotide = true;\r
-\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
+ HiddenSequences hiddenSequences = new HiddenSequences(this);\r
+\r
\r
/** Make an alignment from an array of Sequences.\r
*\r
*/\r
public Alignment(SequenceI[] seqs)\r
{\r
- int i=0, iSize = seqs.length, j, jSize;\r
- while(isNucleotide && i<iSize)\r
- {\r
- jSize = seqs[i].getLength();\r
- for(j=0; j<jSize; j++)\r
- {\r
- if(!jalview.schemes.ResidueProperties.nucleotideHash.containsKey(seqs[i].getSequence(j, j+1))\r
- && !jalview.util.Comparison.isGap(seqs[i].getSequence().charAt(j)))\r
- {\r
- isNucleotide = false;\r
- break;\r
- }\r
- }\r
- i++;\r
- }\r
+ int i=0;\r
+\r
+ if( jalview.util.Comparison.isNucleotide(seqs))\r
+ type = NUCLEOTIDE;\r
+ else\r
+ type = PROTEIN;\r
\r
sequences = new Vector();\r
\r
for (i = 0; i < seqs.length; i++)\r
{\r
sequences.addElement(seqs[i]);\r
+\r
+ if(seqs[i].getDatasetSequence()!=null\r
+ && seqs[i].getDatasetSequence().getAnnotation()!=null)\r
+ {\r
+\r
+ for(int a=0; a<seqs[i].getDatasetSequence().getAnnotation().length; a++)\r
+ {\r
+ this.addAnnotation(seqs[i].getDatasetSequence().getAnnotation()[a], seqs[i]);\r
+ }\r
+ }\r
}\r
\r
getWidth();\r
*/\r
public void trimLeft(int i)\r
{\r
- for (int j = 0; j < getHeight(); j++)\r
+ int j, jSize = getHeight();\r
+ for (j = 0; j < jSize; j++)\r
{\r
SequenceI s = getSequenceAt(j);\r
int newstart = s.findPosition(i);\r
\r
- s.setStart(newstart);\r
- s.setSequence(s.getSequence().substring(i));\r
+ if(i>s.getLength())\r
+ {\r
+ sequences.removeElement(s);\r
+ j--;\r
+ jSize--;\r
+ }\r
+ else\r
+ {\r
+ s.setStart(newstart);\r
+ s.setSequence(s.getSequence().substring(i));\r
+ }\r
}\r
}\r
\r
int newend = s.findPosition(i);\r
\r
s.setEnd(newend);\r
- s.setSequence(s.getSequence().substring(0, i + 1));\r
+ if(s.getLength()>i)\r
+ s.setSequence(s.getSequence().substring(0, i + 1));\r
}\r
}\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
\r
while (i < sequences.size())\r
{\r
- SequenceI s = getSequenceAt(i);\r
-\r
- if (s.getName().equals(name))\r
+ if (getSequenceAt(i).getName().equals(name))\r
{\r
- return s;\r
+ return getSequenceAt(i);\r
}\r
\r
i++;\r
return null;\r
}\r
\r
- /** */\r
- public SequenceI findbyDisplayId(String name)\r
- {\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- SequenceI s = getSequenceAt(i);\r
-\r
- if (s.getDisplayId().equals(name))\r
- {\r
- return s;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return null;\r
- }\r
\r
/** */\r
public int findIndex(SequenceI s)\r
}\r
\r
/**\r
+ *\r
+ * @param aa AlignmentAnnotation\r
+ * @param seqRef The sequence to associate this annotation with\r
+ * @return The adjusted AlignmentAnnotation, with dataset sequence and annotation added\r
+ */\r
+ public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef)\r
+ {\r
+ if(seqRef!=null)\r
+ {\r
+ //We can only add Annotations to the dataset sequences\r
+ if(seqRef.getDatasetSequence()==null)\r
+ {\r
+ setDataset(null);\r
+ }\r
+\r
+ AlignmentAnnotation [] old = seqRef.getDatasetSequence().getAnnotation();\r
+\r
+ //First check if this is a new annotation or not. If it is new,\r
+ //we must add the annotation to the dataset\r
+ boolean newAnnotation = true;\r
+ if(seqRef.getDatasetSequence().getAnnotation()!=null)\r
+ {\r
+ for(int a=0; a<old.length; a++)\r
+ {\r
+ if(old[a] == aa)\r
+ {\r
+\r
+ newAnnotation = false;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ if(newAnnotation)\r
+ {\r
+ seqRef.getDatasetSequence().addAlignmentAnnotation(aa);\r
+ }\r
+\r
+ AlignmentAnnotation copy = null;\r
+ if (aa.graph > 0)\r
+ copy = new AlignmentAnnotation(\r
+ aa.label, aa.description, aa.annotations, aa.graphMin,\r
+ aa.graphMax, aa.graph\r
+ );\r
+ else\r
+ copy = new AlignmentAnnotation(\r
+ aa.label, aa.description, aa.annotations\r
+ );\r
+\r
+ copy.datasetAnnotation = aa;\r
+\r
+ addAnnotation(copy);\r
+\r
+ copy.sequenceRef = seqRef;\r
+\r
+ return copy;\r
+ }\r
+ else\r
+ {\r
+ addAnnotation(aa);\r
+ return aa;\r
+ }\r
+ }\r
+\r
+ public void adjustSequenceAnnotations()\r
+ {\r
+ if(annotations!=null)\r
+ {\r
+ for (int a = 0; a < annotations.length; a++)\r
+ {\r
+ if (annotations[a].sequenceRef != null)\r
+ {\r
+ annotations[a].adjustForAlignment();\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
* DOCUMENT ME!\r
*\r
* @param aa DOCUMENT ME!\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
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
+\r
+ temp[aSize-1] = aa;\r
+\r
int i = 0;\r
\r
if (aSize > 1)\r
{\r
- for (i = 0; i < (aSize - 1); i++)\r
+ for (i = 0; i < (aSize-1); i++)\r
{\r
temp[i] = annotations[i];\r
}\r
}\r
\r
- temp[i] = aa;\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
public void setNucleotide(boolean b)\r
{\r
- isNucleotide = b;\r
+ if(b)\r
+ type = NUCLEOTIDE;\r
+ else\r
+ type = PROTEIN;\r
}\r
\r
public boolean isNucleotide()\r
{\r
- return isNucleotide;\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).getName(),\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 boolean padGaps() {\r
+ boolean modified=false;\r
+ int Width = getWidth();\r
+ SequenceI current;\r
+ for (int i = 0; i < sequences.size();\r
+ i++)\r
+ {\r
+ current = getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, gapCharacter);\r
+ modified=true;\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