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add HMMER colour scheme
author
TZVanaalten
<TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Fri, 23 Jun 2017 11:52:54 +0000
(12:52 +0100)
committer
TZVanaalten
<TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Fri, 23 Jun 2017 11:52:54 +0000
(12:52 +0100)
src/jalview/datamodel/Alignment.java
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src/jalview/datamodel/AlignmentI.java
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src/jalview/datamodel/AnnotatedCollectionI.java
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src/jalview/datamodel/HiddenMarkovModel.java
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src/jalview/datamodel/SequenceGroup.java
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src/jalview/gui/AlignFrame.java
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src/jalview/schemes/JalviewColourScheme.java
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diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
5d91b36
..
a88995d
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-68,6
+68,8
@@
public class Alignment implements AlignmentI
private List<AlignedCodonFrame> codonFrameList;
private List<AlignedCodonFrame> codonFrameList;
+ HiddenMarkovModel hmm;
+
private void initAlignment(SequenceI[] seqs)
{
groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
private void initAlignment(SequenceI[] seqs)
{
groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
@@
-1959,4
+1961,19
@@
public class Alignment implements AlignmentI
{
hiddenCols = cols;
}
{
hiddenCols = cols;
}
+
+ @Override
+ public HiddenMarkovModel getHMM()
+ {
+
+ return hmm;
+ }
+
+ @Override
+ public void setHMM(HiddenMarkovModel markov)
+ {
+
+ hmm = markov;
+ }
+
}
}
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
2e61f9d
..
948fd1b
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-591,4
+591,6
@@
public interface AlignmentI extends AnnotatedCollectionI
public void setHiddenColumns(HiddenColumns cols);
public void setHiddenColumns(HiddenColumns cols);
+
+
}
}
diff --git
a/src/jalview/datamodel/AnnotatedCollectionI.java
b/src/jalview/datamodel/AnnotatedCollectionI.java
index
2963fd5
..
45a3787
100644
(file)
--- a/
src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/
src/jalview/datamodel/AnnotatedCollectionI.java
@@
-61,4
+61,8
@@
public interface AnnotatedCollectionI extends SequenceCollectionI
* alignment, parent group).
*/
AnnotatedCollectionI getContext();
* alignment, parent group).
*/
AnnotatedCollectionI getContext();
+
+ public HiddenMarkovModel getHMM();
+
+ public void setHMM(HiddenMarkovModel hmm);
}
}
diff --git
a/src/jalview/datamodel/HiddenMarkovModel.java
b/src/jalview/datamodel/HiddenMarkovModel.java
index
f614013
..
e214373
100644
(file)
--- a/
src/jalview/datamodel/HiddenMarkovModel.java
+++ b/
src/jalview/datamodel/HiddenMarkovModel.java
@@
-290,10
+290,22
@@
public class HiddenMarkovModel
int symbolIndex;
int nodeIndex;
Double probability;
int symbolIndex;
int nodeIndex;
Double probability;
+ if (symbol == '-')
+ {
+ return 0d;
+ }
symbolIndex = symbolIndexLookup.get(symbol);
symbolIndex = symbolIndexLookup.get(symbol);
- nodeIndex = nodeLookup.get(alignColumn);
- probability = getNode(nodeIndex).getMatchEmissions().get(symbolIndex);
- return probability;
+ if (nodeLookup.containsKey(alignColumn + 1))
+ {
+ nodeIndex = nodeLookup.get(alignColumn + 1);
+ probability = getNode(nodeIndex).getMatchEmissions().get(symbolIndex);
+ probability = Math.pow(Math.E, -probability);
+ return probability;
+ }
+ else
+ {
+ return 0d;
+ }
}
}
@@
-310,10
+322,23
@@
public class HiddenMarkovModel
int symbolIndex;
int nodeIndex;
Double probability;
int symbolIndex;
int nodeIndex;
Double probability;
+ if (symbol == '-')
+ {
+ return 0d;
+ }
symbolIndex = symbolIndexLookup.get(symbol);
symbolIndex = symbolIndexLookup.get(symbol);
- nodeIndex = nodeLookup.get(alignColumn);
- probability = getNode(nodeIndex).getInsertEmissions().get(symbolIndex);
- return probability;
+ if (nodeLookup.containsKey(alignColumn + 1))
+ {
+ nodeIndex = nodeLookup.get(alignColumn + 1);
+ probability = getNode(nodeIndex).getInsertEmissions()
+ .get(symbolIndex);
+ probability = Math.pow(Math.E, -probability);
+ return probability;
+ }
+ else
+ {
+ return 0d;
+ }
}
}
@@
-332,10
+357,18
@@
public class HiddenMarkovModel
int nodeIndex;
Double probability;
transitionIndex = getTransitionType(transition);
int nodeIndex;
Double probability;
transitionIndex = getTransitionType(transition);
- nodeIndex = nodeLookup.get(alignColumn);
- probability = getNode(nodeIndex).getStateTransitions()
+ if (nodeLookup.containsKey(alignColumn + 1))
+ {
+ nodeIndex = nodeLookup.get(alignColumn + 1);
+ probability = getNode(nodeIndex).getStateTransitions()
.get(transitionIndex);
.get(transitionIndex);
- return probability;
+ probability = Math.pow(Math.E, -probability);
+ return probability;
+ }
+ else
+ {
+ return 0d;
+ }
}
}
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
463b909
..
a1a655e
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-51,6
+51,8
@@
public class SequenceGroup implements AnnotatedCollectionI
boolean colourText = false;
boolean colourText = false;
+ HiddenMarkovModel hmm;
+
/**
* True if the group is defined as a group on the alignment, false if it is
* just a selection.
/**
* True if the group is defined as a group on the alignment, false if it is
* just a selection.
@@
-1457,4
+1459,18
@@
public class SequenceGroup implements AnnotatedCollectionI
{
return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
}
{
return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
}
+
+ @Override
+ public HiddenMarkovModel getHMM()
+ {
+ // TODO Auto-generated method stub
+ return hmm;
+ }
+
+ @Override
+ public void setHMM(HiddenMarkovModel markov)
+ {
+ hmm = markov;
+
+ }
}
}
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
2140ed9
..
080e260
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-4654,7
+4654,13
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
HMMFile hmm = new HMMFile(new FileParse(file, sourceType));
hmm.parse();
{
HMMFile hmm = new HMMFile(new FileParse(file, sourceType));
hmm.parse();
- System.out.println("successful");
+
+ getViewport().getAlignment().setHMM(hmm.getHMM());
+
+
+
+
+
}
else if (FileFormat.Jnet.equals(format))
{
}
else if (FileFormat.Jnet.equals(format))
{
diff --git
a/src/jalview/schemes/JalviewColourScheme.java
b/src/jalview/schemes/JalviewColourScheme.java
index
185d2b4
..
c3a3873
100644
(file)
--- a/
src/jalview/schemes/JalviewColourScheme.java
+++ b/
src/jalview/schemes/JalviewColourScheme.java
@@
-22,7
+22,8
@@
public enum JalviewColourScheme
NucleotideColourScheme.class), PurinePyrimidine(
"Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
RNAHelices("RNA Helices", RNAHelicesColour.class), TCoffee(
NucleotideColourScheme.class), PurinePyrimidine(
"Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
RNAHelices("RNA Helices", RNAHelicesColour.class), TCoffee(
- "T-Coffee Scores", TCoffeeColourScheme.class);
+ "T-Coffee Scores", TCoffeeColourScheme.class),
+ HMMER("HMMER", HMMERColourScheme.class);
// RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
private String name;
// RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
private String name;