X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=bca98cfd34a93eff76fe0562b20c16a777a2dde5;hb=2dcd2b8cfb1b38575c8b2246d59ba1c1a2fb59cd;hp=b905c452ba87dcce2683ded2f74c2ec0fdc5cd36;hpb=d640a8ce605b836b2e6eb1771994d3baef5c31a0;p=jalview.git
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index b905c45..bca98cf 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,267 +1,332 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-package jalview.schemes;
-
-import jalview.analysis.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class ResidueColourScheme implements ColourSchemeI
-{
-
- boolean conservationColouring = false;
- boolean consensusColouring = false;
-
- Color[] colors;
- int threshold = 0;
-
- /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
- protected String ignoreGaps = AAFrequency.PID_GAPS;
-
- /** Consenus as a hashtable array */
- Hashtable [] consensus;
-
- /** Conservation string as a char array */
- char [] conservation;
-
- /** DOCUMENT ME!! */
- int inc = 30;
-
-
- /**
- * Creates a new ResidueColourScheme object.
- *
- * @param colors DOCUMENT ME!
- * @param threshold DOCUMENT ME!
- */
- public ResidueColourScheme(Color[] colours, int threshold)
- {
- this.colors = colours;
- this.threshold = threshold;
- }
-
- /**
- * Creates a new ResidueColourScheme object.
- */
- public ResidueColourScheme()
- {
- }
-
- /**
- * Find a colour without an index in a sequence
- */
- public Color findColour(String aa)
- {
- return colors[ResidueProperties.aaIndex[aa.charAt(0)]];
- }
-
-
-
- public Color findColour(String s, int j)
- {
- Color currentColour;
- int index = ResidueProperties.aaIndex[s.charAt(0)];
-
- if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
- {
- currentColour = colors[index];
- }
- else
- {
- currentColour = Color.white;
- }
-
- if(conservationColouring)
- currentColour = applyConservation(currentColour, j);
-
-
- return currentColour;
- }
-
-
- /**
- * Get the percentage threshold for this colour scheme
- *
- * @return Returns the percentage threshold
- */
- public int getThreshold()
- {
- return threshold;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param ct DOCUMENT ME!
- */
- public void setThreshold(int ct, boolean ignoreGaps)
- {
- threshold = ct;
- if(ignoreGaps)
- this.ignoreGaps = AAFrequency.PID_NOGAPS;
- else
- this.ignoreGaps = AAFrequency.PID_GAPS;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param j DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean aboveThreshold(String s, int j)
- {
- char c = s.charAt(0);
- if ('a' <= c && c <= 'z')
- {
- // TO UPPERCASE !!!
- //Faster than toUpperCase
- c -= ('a' - 'A');
- s = String.valueOf(c);
- }
-
- if (consensus == null || consensus[j] == null)
- return false;
-
- if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
- consensus[j].contains(s))
- {
- if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
- {
- return true;
- }
- }
-
- return false;
- }
-
-
- public boolean conservationApplied()
- {
- return conservationColouring;
- }
-
- public void setConservationInc(int i)
- {
- inc = i;
- }
-
- public int getConservationInc()
- {
- return inc;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param consensus DOCUMENT ME!
- */
- public void setConsensus(Hashtable [] consensus)
- {
- if(consensus==null)
- return;
-
- this.consensus = consensus;
- }
-
-
-
- public void setConservation(Conservation cons)
- {
- if(cons==null)
- {
- conservationColouring = false;
- conservation = null;
- }
- else
- {
- conservationColouring = true;
- int i, iSize = cons.getConsSequence().getLength();
- conservation = new char[iSize];
- for (i = 0; i < iSize; i++)
- conservation[i] = cons.getConsSequence().getCharAt(i);
- }
-
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
-
- Color applyConservation(Color currentColour, int i)
- {
-
- if ((conservation[i] != '*') && (conservation[i] != '+'))
- {
- if(jalview.util.Comparison.isGap(conservation[i]))
- {
- currentColour = Color.white;
- }
- else
- {
- float t = 11 - (conservation[i] - '0');
- if(t==0)
- {
- return Color.white;
- }
-
- int red = currentColour.getRed();
- int green = currentColour.getGreen();
- int blue = currentColour.getBlue();
-
- int dr = 255 - red;
- int dg = 255 - green;
- int db = 255 - blue;
-
- dr *= t / 10f;
- dg *= t / 10f;
- db *= t / 10f;
-
- red += (inc / 20f) * dr;
- green += (inc / 20f) * dg;
- blue += (inc / 20f) * db;
-
- if (red > 255 || green > 255 || blue > 255)
- currentColour = Color.white;
- else
- currentColour = new Color(red, green, blue);
- }
- }
- return currentColour;
- }
-
-
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
+ final int[] symbolIndex;
+
+ boolean conservationColouring = false;
+
+ Color[] colors = null;
+
+ int threshold = 0;
+
+ /* Set when threshold colouring to either pid_gaps or pid_nogaps */
+ protected String ignoreGaps = AAFrequency.PID_GAPS;
+
+ /** Consenus as a hashtable array */
+ Hashtable[] consensus;
+
+ /** Conservation string as a char array */
+ char[] conservation;
+
+ int conservationLength = 0;
+
+ /** DOCUMENT ME!! */
+ int inc = 30;
+
+ /**
+ * Creates a new ResidueColourScheme object.
+ *
+ * @param final int[] index table into colors (ResidueProperties.naIndex or
+ * ResidueProperties.aaIndex)
+ * @param colors
+ * colours for symbols in sequences
+ * @param threshold
+ * threshold for conservation shading
+ */
+ public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours,
+ int threshold)
+ {
+ symbolIndex = aaOrnaIndex;
+ this.colors = colours;
+ this.threshold = threshold;
+ }
+
+ /**
+ * 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)
+ {
+ return colors == null ? Color.white : colors[symbolIndex[c]];
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color currentColour;
+
+ if (colors != null && symbolIndex != null && (threshold == 0)
+ || aboveThreshold(c, j))
+ {
+ currentColour = colors[symbolIndex[c]];
+ }
+ else
+ {
+ currentColour = Color.white;
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+
+ /**
+ * Get the percentage threshold for this colour scheme
+ *
+ * @return Returns the percentage threshold
+ */
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ct
+ * DOCUMENT ME!
+ */
+ public void setThreshold(int ct, boolean ignoreGaps)
+ {
+ threshold = ct;
+ if (ignoreGaps)
+ {
+ this.ignoreGaps = AAFrequency.PID_NOGAPS;
+ }
+ else
+ {
+ this.ignoreGaps = AAFrequency.PID_GAPS;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean aboveThreshold(char c, int j)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ // TO UPPERCASE !!!
+ // Faster than toUpperCase
+ c -= ('a' - 'A');
+ }
+
+ if (consensus == null || consensus.length < j || consensus[j] == null)
+ {
+ return false;
+ }
+
+ if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1)
+ && consensus[j].contains(String.valueOf(c)))
+ {
+ if (((Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+ {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ public boolean conservationApplied()
+ {
+ return conservationColouring;
+ }
+
+ @Override
+ public void setConservationApplied(boolean conservationApplied)
+ {
+ conservationColouring = conservationApplied;
+ }
+
+ public void setConservationInc(int i)
+ {
+ inc = i;
+ }
+
+ public int getConservationInc()
+ {
+ return inc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param consensus
+ * DOCUMENT ME!
+ */
+ public void setConsensus(Hashtable[] consensus)
+ {
+ if (consensus == null)
+ {
+ return;
+ }
+
+ this.consensus = consensus;
+ }
+
+ public void setConservation(Conservation cons)
+ {
+ if (cons == null)
+ {
+ conservationColouring = false;
+ conservation = null;
+ }
+ else
+ {
+ conservationColouring = true;
+ int i, iSize = cons.getConsSequence().getLength();
+ conservation = new char[iSize];
+ for (i = 0; i < iSize; i++)
+ {
+ conservation[i] = cons.getConsSequence().getCharAt(i);
+ }
+ conservationLength = conservation.length;
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ * @param i
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+
+ Color applyConservation(Color currentColour, int i)
+ {
+
+ if ((conservationLength > i) && (conservation[i] != '*')
+ && (conservation[i] != '+'))
+ {
+ if (jalview.util.Comparison.isGap(conservation[i]))
+ {
+ currentColour = Color.white;
+ }
+ else
+ {
+ float t = 11 - (conservation[i] - '0');
+ if (t == 0)
+ {
+ return Color.white;
+ }
+
+ int red = currentColour.getRed();
+ int green = currentColour.getGreen();
+ int blue = currentColour.getBlue();
+
+ int dr = 255 - red;
+ int dg = 255 - green;
+ int db = 255 - blue;
+
+ dr *= t / 10f;
+ dg *= t / 10f;
+ db *= t / 10f;
+
+ red += (inc / 20f) * dr;
+ green += (inc / 20f) * dg;
+ blue += (inc / 20f) * db;
+
+ if (red > 255 || green > 255 || blue > 255)
+ {
+ currentColour = Color.white;
+ }
+ else
+ {
+ currentColour = new Color(red, green, blue);
+ }
+ }
+ }
+ return currentColour;
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map hiddenReps)
+ {
+ }
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map hiddenRepSequences)
+ {
+ try
+ {
+ return getClass().newInstance();
+ } catch (Exception q)
+ {
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_cannot_duplicate_colour_scheme",
+ new String[] { getClass().getName() }), q);
+ }
+ }
+}