-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class ResidueColourScheme implements ColourSchemeI\r
-{\r
- Color[] colors;\r
- int threshold = 0;\r
-\r
- /* Set when threshold colouring to either pid_gaps or pid_nogaps*/\r
- protected String ignoreGaps = "pid_gaps";\r
-\r
- /** DOCUMENT ME!! */\r
- public Hashtable [] consensus;\r
-\r
- /**\r
- * Creates a new ResidueColourScheme object.\r
- *\r
- * @param colors DOCUMENT ME!\r
- * @param threshold DOCUMENT ME!\r
- */\r
- public ResidueColourScheme(Color[] colors, int threshold)\r
- {\r
- this.colors = colors;\r
- this.threshold = threshold;\r
- }\r
-\r
- /**\r
- * Creates a new ResidueColourScheme object.\r
- */\r
- public ResidueColourScheme()\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param consensus DOCUMENT ME!\r
- */\r
- public void setConsensus(Vector vconsensus)\r
- {\r
- int i, iSize=vconsensus.size();\r
- consensus = new Hashtable[iSize];\r
- for(i=0; i<iSize; i++)\r
- consensus[i] = (Hashtable)vconsensus.elementAt(i);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param aa DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String aa)\r
- {\r
- return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String s, int j)\r
- {\r
- if ((threshold == 0) || aboveThreshold(s, j))\r
- {\r
- return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];\r
- }\r
- else\r
- {\r
- return Color.white;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getThreshold()\r
- {\r
- return threshold;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ct DOCUMENT ME!\r
- */\r
- public void setThreshold(int ct, boolean ignoreGaps)\r
- {\r
- threshold = ct;\r
- if(ignoreGaps)\r
- this.ignoreGaps = "pid_nogaps";\r
- else\r
- this.ignoreGaps = "pid_gaps";\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean aboveThreshold(String s, int j)\r
- {\r
- if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&\r
- consensus[j].contains(s))\r
- {\r
- float ratio = ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
-\r
- if (ratio >= threshold)\r
- {\r
- return true;\r
- }\r
- }\r
-\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.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+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 (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;
+ }
+ if (ac == null)
+ {
+ return true;
+ }
+ /*
+ * pop-up menu on selection group before group created
+ * (no alignment context)
+ */
+ // TODO: add nucleotide flag to SequenceGroup?
+ if (ac instanceof SequenceGroup && ac.getContext() == null)
+ {
+ return true;
+ }
+
+ /*
+ * inspect the data context (alignment) for residue type
+ */
+ boolean nucleotide = ac.isNucleotide();
+
+ /*
+ * 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