-/*\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
-public class ResidueColourScheme implements ColourSchemeI {\r
- Color[] colors;\r
- int threshold = 0;\r
- public Vector consensus;\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 void setConsensus(Vector consensus) {\r
- this.consensus = consensus;\r
- }\r
-\r
- public Color findColour(String aa) {\r
- return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];\r
- }\r
-\r
- public Color findColour(String s, int j) {\r
- if ((threshold == 0) || aboveThreshold(s, j)) {\r
- return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];\r
- } else {\r
- return Color.white;\r
- }\r
- }\r
-\r
- public int getThreshold() {\r
- return threshold;\r
- }\r
-\r
- public void setThreshold(int ct) {\r
- threshold = ct;\r
- }\r
-\r
- public boolean aboveThreshold(String s, int j) {\r
- Hashtable hash = (Hashtable) consensus.elementAt(j);\r
-\r
- if ((((Integer) hash.get("maxCount")).intValue() != -1) &&\r
- hash.contains(s)) {\r
- //// resCount//////////////////// ///////////////seq count////////////\r
- double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(\r
- "size")).intValue();\r
-\r
- if (sc >= threshold) {\r
- return true;\r
- }\r
- }\r
-\r
- return false;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.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<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ }
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> 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);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff