X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FTCoffeeColourScheme.java;h=db85cc842445951459e9a5166ec5e63a6f6694f1;hb=155a17a423e980849fd4dc5f857da1a72b0010b9;hp=1c8e469824bbe5190f9b96988076457c83187e02;hpb=fb27f86492eb06fc39b0578e1c31de8b4c26491a;p=jalview.git
diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 1c8e469..db85cc8 100644
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -1,24 +1,26 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
@@ -30,8 +32,8 @@ import jalview.io.TCoffeeScoreFile;
import java.awt.Color;
import java.util.ArrayList;
import java.util.IdentityHashMap;
+import java.util.List;
import java.util.Map;
-import java.util.TreeMap;
/**
* Defines the color score for T-Coffee MSA
@@ -44,21 +46,15 @@ import java.util.TreeMap;
*/
public class TCoffeeColourScheme extends ResidueColourScheme
{
+ IdentityHashMap seqMap;
- static final Color[] colors =
- { new Color(102, 102, 255), // #6666FF
- new Color(0, 255, 0), // #00FF00
- new Color(102, 255, 0), // #66FF00
- new Color(204, 255, 0), // #CCFF00
- new Color(255, 255, 0), // #FFFF00
- new Color(255, 204, 0), // #FFCC00
- new Color(255, 153, 0), // #FF9900
- new Color(255, 102, 0), // #FF6600
- new Color(255, 51, 0), // #FF3300
- new Color(255, 34, 0) // #FF2000
- };
+ /**
+ * Default constructor (required for Class.newInstance())
+ */
+ public TCoffeeColourScheme()
+ {
- IdentityHashMap seqMap;
+ }
/**
* the color scheme needs to look at the alignment to get and cache T-COFFEE
@@ -72,6 +68,13 @@ public class TCoffeeColourScheme extends ResidueColourScheme
alignmentChanged(alignment, null);
}
+ /**
+ * Finds the TCoffeeScore annotation (if any) for each sequence and notes the
+ * annotation colour for each column position. The colours are fixed for
+ * scores 0-9 and are set when annotation is parsed.
+ *
+ * @see TCoffeeScoreFile#annotateAlignment(AlignmentI, boolean)
+ */
@Override
public void alignmentChanged(AnnotatedCollectionI alignment,
Map hiddenReps)
@@ -81,11 +84,17 @@ public class TCoffeeColourScheme extends ResidueColourScheme
// assume only one set of TCOFFEE scores - but could have more than one
// potentially.
- ArrayList annots = new ArrayList();
+ List annots = new ArrayList<>();
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
- seqMap = new IdentityHashMap();
- AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
+ seqMap = new IdentityHashMap<>();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
+ ? alignment
+ : alignment.getContext();
+ if (alcontext == null)
+ {
+ return;
+ }
int w = 0;
for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
@@ -115,9 +124,12 @@ public class TCoffeeColourScheme extends ResidueColourScheme
@Override
public Color findColour(char c, int j, SequenceI seq)
{
- Color[] cols;
-
- if (seqMap == null || (cols = seqMap.get(seq)) == null)
+ if (seqMap == null)
+ {
+ return Color.WHITE;
+ }
+ Color[] cols = seqMap.get(seq);
+ if (cols == null)
{
// see above TODO about computing a colour for each residue in each
// column: cc = _rcols[i][indexFor[c]];
@@ -130,11 +142,40 @@ public class TCoffeeColourScheme extends ResidueColourScheme
}
return cols[j];
}
-
+
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
- Map hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
return new TCoffeeColourScheme(sg);
}
+
+ /**
+ * Answers true if the data has TCoffee score annotation
+ */
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac
+ : ac.getContext();
+ if (alcontext == null)
+ {
+ return false;
+ }
+ Iterable anns = alcontext
+ .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE);
+ return anns.iterator().hasNext();
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.TCoffee.toString();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}