JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / examples / groovy / colourSchemes.groovy

diff --git a/examples/groovy/colourSchemes.groovy b/examples/groovy/colourSchemes.groovy
deleted file mode 100644 (file)
index eb40cc6..0000000
--- a/examples/groovy/colourSchemes.groovy
+++ /dev/null
@@ -1,156 +0,0 @@
-import java.awt.Color;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemes;
-import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.api.AlignViewportI
-
-/*
- * Example script that registers two new alignment colour schemes
- */
-
-/*
- * Closure that defines a colour scheme where consensus residues are pink,
- * other residues are red in odd columns and blue in even columns, and
- * gaps are yellow  
- */
-def candy
-candy = { ->
-  [
-    /*
-     * name shown in the colour menu
-     */
-    getSchemeName: { -> 'candy' },
-    
-    /*
-     * to make a new instance for each alignment view
-     */
-    getInstance: { view, coll -> candy() },
-    
-    /*
-     * method only needed if colour scheme has to recalculate
-     * values when an alignment is modified
-     */
-    alignmentChanged: { AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> },
-    
-    /*
-     * determine colour for a residue at an aligned position of a
-     * sequence, given consensus residue(s) for the column and the
-     * consensus percentage identity score for the column
-     */
-    findColour: { char res, int col, SequenceI seq, String consensus, float pid -> 
-        if (res == ' ' || res == '-' || res == '.') 
-        {
-            Color.yellow
-        } else if (consensus.contains(String.valueOf(res)))
-        {
-            Color.pink
-        } else if (col % 2 == 0) 
-        {
-            Color.blue
-        } else 
-        {
-            Color.red
-        }
-    },
-    
-    /*
-     * true means applicable to nucleotide or peptide data
-     */
-    isApplicableTo: {AnnotatedCollectionI coll -> true},
-    
-    /*
-     * simple colour schemes are those that depend on the residue
-     * only (these are also available to colour structure viewers)
-     */
-    isSimple: { false }
- ] as ColourSchemeI
-}
-
-/*
- * A closure that defines a colour scheme graduated 
- * (approximately) by amino acid weight
- * here from lightest (G) Blue, to heaviest (W) Red
- */
-def makeColour = { weight -> 
-    minWeight = 75 // Glycine
-    maxWeight = 204 // Tryptophan
-    int i = 255 * (weight - minWeight) / (maxWeight - minWeight);
-    new Color(i, 0, 255-i);
-}
-def byWeight
-byWeight = { ->
-  [
-    getSchemeName: { 'By Weight' },
-    // this colour scheme is peptide-specific:
-    isApplicableTo: { coll -> !coll.isNucleotide() },
-    alignmentChanged: { coll, map -> },
-    getInstance: { view, coll -> byWeight() },
-    isSimple: { true },
-    findColour: {res, col, seq, consensus, pid -> 
-        switch (res) {
-          case ' ':
-          case '-':
-          case '.':
-            Color.white
-             break
-          case 'A':
-            makeColour(89)
-            break
-          case 'R':
-            makeColour(174)
-            break
-          case 'N':
-          case 'D':
-          case 'B':
-          case 'I':
-          case 'L':
-            makeColour(132)
-            break
-          case 'C':
-            makeColour(121)
-            break
-          case 'Q':
-          case 'E':
-          case 'Z':
-          case 'K':
-          case 'M':
-            makeColour(146)
-            break
-          case 'G':
-            makeColour(75)
-            break
-          case 'H':
-            makeColour(155)
-            break
-          case 'F':
-            makeColour(165)
-            break
-          case 'P':
-            makeColour(115)
-            break
-          case 'S':
-            makeColour(105)
-            break
-          case 'T':
-            makeColour(119)
-            break
-          case 'W':
-            makeColour(204)
-            break
-          case 'Y':
-            makeColour(181)
-            break
-          case 'V':
-            makeColour(117)
-            break
-          default:
-            makeColour(150)
-        }
-      }
-  ] as ColourSchemeI
-}
-
-ColourSchemes.instance.registerColourScheme(candy())
-ColourSchemes.instance.registerColourScheme(byWeight())