-package jalview.schemes;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.jbgui.*;\r
-\r
-import java.util.*;\r
-import java.awt.*;\r
-\r
-public class ResidueColourScheme implements ColourSchemeI {\r
- Color [] colors;\r
- int threshold = 90;\r
-\r
- public ResidueColourScheme(Color[] colors, int threshold) {\r
- this.colors = colors;\r
- this.threshold = threshold;\r
- }\r
-\r
- public ResidueColourScheme() {\r
- }\r
-\r
- public Color findColour(String aa)\r
- {\r
- return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
- }\r
-\r
- public Color findColour(SequenceI seq,String s, int j, Vector aa) {\r
- try {\r
- return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
- } catch (Exception e) {\r
- return Color.white;\r
- }\r
- }\r
-\r
- // aa should maybe be a class\r
- public Color getColour(SequenceI seq, int j,Vector aa) {\r
-\r
- Color c = Color.white;\r
- String s = seq.getSequence(j,j+1);\r
-\r
- if (threshold > 0 && aa != null)\r
- {\r
- if (aboveThreshold(aa,seq,j,threshold))\r
- c = findColour(seq,s,j,aa);\r
- }\r
- else\r
- c = findColour(seq,s,j,aa);\r
-\r
-\r
- return c;\r
- }\r
- public int getThreshold() {\r
- return threshold;\r
- }\r
-\r
- public void setThreshold(int ct) {\r
- threshold = ct;\r
- }\r
-\r
- public Vector getColours(SequenceI s, Vector aa) {\r
- Vector colours = new Vector();\r
-\r
- for (int j = 0; j < s.getLength(); j++)\r
- colours.addElement(getColour(s,j,aa));\r
-\r
- return colours;\r
- }\r
-\r
- public Vector getColours(SequenceGroup sg, Vector aa) {\r
- Vector colours = new Vector();\r
-\r
- for (int j = 0; j < sg.getSize(); j++) {\r
- SequenceI s = sg.getSequenceAt(j);\r
-\r
- for (int i = 0; i < s.getLength();i++) {\r
- colours.addElement(getColour(s,i,aa));\r
- }\r
- }\r
- return colours;\r
- }\r
-\r
- public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {\r
- String s = seq.getSequence(j,j+1);\r
- Hashtable hash = (Hashtable)aa.elementAt(j);\r
-\r
- if (j < aa.size()) {\r
- String maxRes = (String)hash.get("maxResidue");\r
-\r
- double sc = 0;\r
-\r
- if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) {\r
- int maxCount = ((Integer)hash.get("maxCount")).intValue();\r
- int resCount = ((Integer)hash.get(s)).intValue();\r
-\r
- sc = resCount * 100.0 / resCount;\r
-\r
- // This should be isGap somewhere\r
- if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) {\r
- if (sc >= (double)threshold) {\r
- return true;\r
- }\r
- }\r
- }\r
- }\r
- return false;\r
- }\r
-\r
- public boolean canThreshold() {\r
- return true;\r
- }\r
- public boolean isUserDefinable() {\r
- return false;\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * Base class for residue-based colour schemes
+ */
+public abstract class ResidueColourScheme implements ColourSchemeI
+{
+ public static final String NONE = "None";
+
+ public static final String USER_DEFINED = "User Defined";
+
+ /*
+ * lookup up by character value e.g. 'G' to the colors array index
+ * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
+ */
+ final int[] symbolIndex;
+
+ /*
+ * colour for residue characters as indexed by symbolIndex
+ */
+ Color[] colors = null;
+
+ /* Set when threshold colouring to either pid_gaps or pid_nogaps */
+ protected boolean ignoreGaps = false;
+
+ /**
+ * Creates a new ResidueColourScheme object.
+ *
+ * @param final int[] index table into colors (ResidueProperties.naIndex or
+ * ResidueProperties.aaIndex)
+ * @param colors
+ * colours for symbols in sequences
+ */
+ public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours)
+ {
+ symbolIndex = aaOrnaIndex;
+ this.colors = colours;
+ }
+
+ /**
+ * Creates a new ResidueColourScheme object with a lookup table for indexing
+ * the colour map
+ */
+ public ResidueColourScheme(int[] aaOrNaIndex)
+ {
+ symbolIndex = aaOrNaIndex;
+ }
+
+ /**
+ * Creates a new ResidueColourScheme object - default constructor for
+ * non-sequence dependent colourschemes
+ */
+ public ResidueColourScheme()
+ {
+ symbolIndex = null;
+ }
+
+ /**
+ * Find a colour without an index in a sequence
+ */
+ public Color findColour(char c)
+ {
+ Color colour = Color.white;
+
+ if (!Comparison.isGap(c) && colors != null && symbolIndex != null
+ && c < symbolIndex.length
+ && symbolIndex[c] < colors.length)
+ {
+ colour = colors[symbolIndex[c]];
+ }
+
+ return colour;
+ }
+
+ /**
+ * Default is to call the overloaded method that ignores consensus. A colour
+ * scheme that depends on consensus (for example, Blosum62), should override
+ * this method instead.
+ */
+ @Override
+ public Color findColour(char c, int j, SequenceI seq,
+ String consensusResidue, float pid)
+ {
+ return findColour(c, j, seq);
+ }
+
+ /**
+ * Default implementation looks up the residue colour in a fixed scheme, or
+ * returns White if not found. Override this method for a colour scheme that
+ * depends on the column position or sequence.
+ *
+ * @param c
+ * @param j
+ * @param seq
+ * @return
+ */
+ protected Color findColour(char c, int j, SequenceI seq)
+ {
+ return findColour(c);
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ }
+
+ /**
+ * Answers false if the colour scheme is nucleotide or peptide specific, and
+ * the data does not match, else true. Override to modify or extend this test
+ * as required.
+ */
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ if (!isPeptideSpecific() && !isNucleotideSpecific())
+ {
+ return true;
+ }
+
+ /*
+ * inspect the data context (alignment) for residue type
+ */
+ boolean nucleotide = false;
+ if (ac instanceof AlignmentI)
+ {
+ nucleotide = ((AlignmentI) ac).isNucleotide();
+ }
+ else
+ {
+ AnnotatedCollectionI context = ac.getContext();
+ if (context instanceof AlignmentI)
+ {
+ nucleotide = ((AlignmentI) context).isNucleotide();
+ }
+ else
+ {
+ // not sure what's going on, play safe
+ return true;
+ }
+ }
+
+ /*
+ * does data type match colour scheme type?
+ */
+ return (nucleotide && isNucleotideSpecific())
+ || (!nucleotide && isPeptideSpecific());
+ }
+
+ /**
+ * Answers true if the colour scheme is normally only for peptide data
+ *
+ * @return
+ */
+ public boolean isPeptideSpecific()
+ {
+ return false;
+ }
+
+ /**
+ * Answers true if the colour scheme is normally only for nucleotide data
+ *
+ * @return
+ */
+ public boolean isNucleotideSpecific()
+ {
+ return false;
+ }
+
+ /**
+ * Default method returns true. Override this to return false in colour
+ * schemes that are not determined solely by the sequence symbol.
+ */
+ @Override
+ public boolean isSimple()
+ {
+ return true;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff