/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.util.*;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
-import java.awt.*;
+import java.awt.Color;
+import java.util.List;
+import java.util.Map;
-import jalview.datamodel.*;
-
-public class ClustalxColourScheme
- extends ResidueColourScheme // implements IParameterizable
+public class ClustalxColourScheme extends ResidueColourScheme
{
- public static Hashtable colhash = new Hashtable();
- Hashtable[] cons;
- int[][] cons2;
- ConsensusColour[] colours;
- ConsensusColour[] ResidueColour;
- int size;
- Consensus[] conses = new Consensus[32];
- Vector colourTable = new Vector();
- private boolean includeGaps=true;
-
- {
- colhash.put("RED", new Color( (float) 0.9, (float) 0.2, (float) 0.1));
- colhash.put("BLUE", new Color( (float) 0.5, (float) 0.7, (float) 0.9));
- colhash.put("GREEN", new Color( (float) 0.1, (float) 0.8, (float) 0.1));
- colhash.put("ORANGE", new Color( (float) 0.9, (float) 0.6, (float) 0.3));
- colhash.put("CYAN", new Color( (float) 0.1, (float) 0.7, (float) 0.7));
- colhash.put("PINK", new Color( (float) 0.9, (float) 0.5, (float) 0.5));
- colhash.put("MAGENTA", new Color( (float) 0.8, (float) 0.3, (float) 0.8));
- colhash.put("YELLOW", new Color( (float) 0.8, (float) 0.8, (float) 0.0));
- }
+ private static final int EIGHTY_FIVE = 85;
+
+ private static final int FIFTY = 50;
- public ClustalxColourScheme(Vector seqs, int maxWidth)
+ private static final int EIGHTY = 80;
+
+ private static final int SIXTY = 60;
+
+ enum ClustalColour
{
- resetClustalX(seqs, maxWidth);
+ RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
+ ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
+ PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
+ YELLOW(0.8f, 0.8f, 0.0f);
+
+ final Color colour;
+
+ ClustalColour(float r, float g, float b)
+ {
+ colour = new Color(r, g, b);
+ }
}
- public void resetClustalX(Vector seqs, int maxWidth)
+ private class ConsensusColour
{
- cons2 = new int[maxWidth][24];
- includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to get the current setting of the includeGaps param.
- int start = 0;
+ Consensus[] cons;
+
+ Color c;
- // Initialize the array
- for (int j = 0; j < 24; j++)
+ public ConsensusColour(ClustalColour col, Consensus[] conses)
{
- for (int i = 0; i < maxWidth; i++)
- {
- cons2[i][j] = 0;
- }
+ this.cons = conses;
+ this.c = col.colour;
}
+ }
- int res;
- int i;
- int j = 0;
- char[] seq;
+ private int[][] cons2;
- while (j < seqs.size())
- {
- seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
+ private ConsensusColour[] colours;
+
+ private ConsensusColour[] residueColour;
+
+ private int size;
+
+ private Consensus[] conses = new Consensus[32];
- int end_j = seq.length - 1;
+ private boolean includeGaps = true;
+
+ /**
+ * Default constructor (required for Class.newInstance())
+ */
+ public ClustalxColourScheme()
+ {
+
+ }
- for (i = start; i <= end_j; i++)
+ public ClustalxColourScheme(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ alignmentChanged(alignment, hiddenReps);
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ int maxWidth = alignment.getWidth();
+ List<SequenceI> seqs = alignment.getSequences(hiddenReps);
+ cons2 = new int[maxWidth][24];
+ includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
+ // get the current setting of the
+ // includeGaps param.
+ int res = 0;
+
+ for (SequenceI sq : seqs)
+ {
+ int end_j = sq.getLength() - 1;
+ int length = sq.getLength();
+
+ for (int i = 0; i <= end_j; i++)
{
- if ( (seq.length - 1) < i)
+ if (length - 1 < i)
{
res = 23;
}
else
{
- res = ResidueProperties.aaIndex[seq[i]];
+ res = ResidueProperties.aaIndex[sq.getCharAt(i)];
}
-
cons2[i][res]++;
}
-
- j++;
}
-
+
this.size = seqs.size();
makeColours();
}
- public void makeColours()
+ void makeColours()
{
- conses[0] = new Consensus("WLVIMAFCYHP", 60);
- conses[1] = new Consensus("WLVIMAFCYHP", 80);
- conses[2] = new Consensus("ED", 50);
- conses[3] = new Consensus("KR", 60);
- conses[4] = new Consensus("G", 50);
- conses[5] = new Consensus("N", 50);
- conses[6] = new Consensus("QE", 50);
- conses[7] = new Consensus("P", 50);
- conses[8] = new Consensus("TS", 50);
-
- conses[26] = new Consensus("A", 85);
- conses[27] = new Consensus("C", 85);
- conses[10] = new Consensus("E", 85);
- conses[11] = new Consensus("F", 85);
- conses[12] = new Consensus("G", 85);
- conses[13] = new Consensus("H", 85);
- conses[14] = new Consensus("I", 85);
- conses[15] = new Consensus("L", 85);
- conses[16] = new Consensus("M", 85);
- conses[17] = new Consensus("N", 85);
- conses[18] = new Consensus("P", 85);
- conses[19] = new Consensus("Q", 85);
- conses[20] = new Consensus("R", 85);
- conses[21] = new Consensus("S", 85);
- conses[22] = new Consensus("T", 85);
- conses[23] = new Consensus("V", 85);
- conses[24] = new Consensus("W", 85);
- conses[25] = new Consensus("Y", 85);
- conses[28] = new Consensus("K", 85);
- conses[29] = new Consensus("D", 85);
+ conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
+ conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
+ conses[2] = new Consensus("ED", FIFTY);
+ conses[3] = new Consensus("KR", SIXTY);
+ conses[4] = new Consensus("G", FIFTY);
+ conses[5] = new Consensus("N", FIFTY);
+ conses[6] = new Consensus("QE", FIFTY);
+ conses[7] = new Consensus("P", FIFTY);
+ conses[8] = new Consensus("TS", FIFTY);
+
+ conses[26] = new Consensus("A", EIGHTY_FIVE);
+ conses[27] = new Consensus("C", EIGHTY_FIVE);
+ conses[10] = new Consensus("E", EIGHTY_FIVE);
+ conses[11] = new Consensus("F", EIGHTY_FIVE);
+ conses[12] = new Consensus("G", EIGHTY_FIVE);
+ conses[13] = new Consensus("H", EIGHTY_FIVE);
+ conses[14] = new Consensus("I", EIGHTY_FIVE);
+ conses[15] = new Consensus("L", EIGHTY_FIVE);
+ conses[16] = new Consensus("M", EIGHTY_FIVE);
+ conses[17] = new Consensus("N", EIGHTY_FIVE);
+ conses[18] = new Consensus("P", EIGHTY_FIVE);
+ conses[19] = new Consensus("Q", EIGHTY_FIVE);
+ conses[20] = new Consensus("R", EIGHTY_FIVE);
+ conses[21] = new Consensus("S", EIGHTY_FIVE);
+ conses[22] = new Consensus("T", EIGHTY_FIVE);
+ conses[23] = new Consensus("V", EIGHTY_FIVE);
+ conses[24] = new Consensus("W", EIGHTY_FIVE);
+ conses[25] = new Consensus("Y", EIGHTY_FIVE);
+ conses[28] = new Consensus("K", EIGHTY_FIVE);
+ conses[29] = new Consensus("D", EIGHTY_FIVE);
conses[30] = new Consensus("G", 0);
conses[31] = new Consensus("P", 0);
colours = new ConsensusColour[11];
Consensus[] tmp8 = new Consensus[1];
- tmp8[0] = conses[30]; //G
- colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8);
+ tmp8[0] = conses[30]; // G
+ colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8);
Consensus[] tmp9 = new Consensus[1];
- tmp9[0] = conses[31]; //P
- colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9);
+ tmp9[0] = conses[31]; // P
+ colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9);
Consensus[] tmp10 = new Consensus[1];
- tmp10[0] = conses[27]; //C
- colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8);
+ tmp10[0] = conses[27]; // C
+ colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8);
Consensus[] tmp1 = new Consensus[14];
- tmp1[0] = conses[0]; //%
- tmp1[1] = conses[1]; //#
- tmp1[2] = conses[26]; //A
- tmp1[3] = conses[27]; //C
- tmp1[4] = conses[11]; //F
- tmp1[5] = conses[13]; //H
- tmp1[6] = conses[14]; //I
- tmp1[7] = conses[15]; //L
- tmp1[8] = conses[16]; //M
- tmp1[9] = conses[23]; //V
- tmp1[10] = conses[24]; //W
- tmp1[11] = conses[25]; //Y
- tmp1[12] = conses[18]; //P
- tmp1[13] = conses[19]; //p
- colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1);
-
- colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1);
+ tmp1[0] = conses[0]; // %
+ tmp1[1] = conses[1]; // #
+ tmp1[2] = conses[26]; // A
+ tmp1[3] = conses[27]; // C
+ tmp1[4] = conses[11]; // F
+ tmp1[5] = conses[13]; // H
+ tmp1[6] = conses[14]; // I
+ tmp1[7] = conses[15]; // L
+ tmp1[8] = conses[16]; // M
+ tmp1[9] = conses[23]; // V
+ tmp1[10] = conses[24]; // W
+ tmp1[11] = conses[25]; // Y
+ tmp1[12] = conses[18]; // P
+ tmp1[13] = conses[19]; // p
+ colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1);
+
+ colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1);
Consensus[] tmp2 = new Consensus[5];
- tmp2[0] = conses[8]; //t
- tmp2[1] = conses[21]; //S
- tmp2[2] = conses[22]; //T
- tmp2[3] = conses[0]; //%
- tmp2[4] = conses[1]; //#
- colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2);
+ tmp2[0] = conses[8]; // t
+ tmp2[1] = conses[21]; // S
+ tmp2[2] = conses[22]; // T
+ tmp2[3] = conses[0]; // %
+ tmp2[4] = conses[1]; // #
+ colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2);
Consensus[] tmp3 = new Consensus[3];
- tmp3[0] = conses[17]; //N
- tmp3[1] = conses[29]; //D
- tmp3[2] = conses[5]; //n
- colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3);
+ tmp3[0] = conses[17]; // N
+ tmp3[1] = conses[29]; // D
+ tmp3[2] = conses[5]; // n
+ colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3);
Consensus[] tmp4 = new Consensus[6];
tmp4[0] = conses[6]; // q = QE
- tmp4[1] = conses[19]; //Q
- tmp4[2] = conses[22]; //E
- tmp4[3] = conses[3]; //+
- tmp4[4] = conses[28]; //K
- tmp4[5] = conses[20]; //R
- colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);
+ tmp4[1] = conses[19]; // Q
+ tmp4[2] = conses[22]; // E
+ tmp4[3] = conses[3]; // +
+ tmp4[4] = conses[28]; // K
+ tmp4[5] = conses[20]; // R
+ colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4);
Consensus[] tmp5 = new Consensus[4];
- tmp5[0] = conses[3]; //+
- tmp5[1] = conses[28]; //K
- tmp5[2] = conses[20]; //R
- tmp5[3] = conses[19]; //Q
- colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5);
-
- Consensus[] tmp6 = new Consensus[5];
- tmp6[0] = conses[3]; //-
- tmp6[1] = conses[29]; //D
- tmp6[2] = conses[10]; //E
- tmp6[3] = conses[6]; //q
- tmp6[4] = conses[19]; //Q
- colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);
+ tmp5[0] = conses[3]; // +
+ tmp5[1] = conses[28]; // K
+ tmp5[2] = conses[20]; // R
+ tmp5[3] = conses[19]; // Q
+ colours[4] = new ConsensusColour(ClustalColour.RED, tmp5);
+
+ Consensus[] tmp6 = new Consensus[6];
+ tmp6[0] = conses[3]; // -
+ tmp6[1] = conses[29]; // D
+ tmp6[2] = conses[10]; // E
+ tmp6[3] = conses[6]; // QE
+ tmp6[4] = conses[19]; // Q
+ tmp6[5] = conses[2]; // DE
+ colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6);
Consensus[] tmp7 = new Consensus[5];
- tmp7[0] = conses[3]; //-
- tmp7[1] = conses[29]; //D
- tmp7[2] = conses[10]; //E
- tmp7[3] = conses[17]; //N
- tmp7[4] = conses[2]; //DE
- colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7);
+ tmp7[0] = conses[3]; // -
+ tmp7[1] = conses[29]; // D
+ tmp7[2] = conses[10]; // E
+ tmp7[3] = conses[17]; // N
+ tmp7[4] = conses[2]; // DE
+ colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7);
// Now attach the ConsensusColours to the residue letters
- ResidueColour = new ConsensusColour[20];
- ResidueColour[0] = colours[0]; // A
- ResidueColour[1] = colours[4]; // R
- ResidueColour[2] = colours[2]; // N
- ResidueColour[3] = colours[6]; // D
- ResidueColour[4] = colours[0]; // C
- ResidueColour[5] = colours[3]; // Q
- ResidueColour[6] = colours[5]; // E
- ResidueColour[7] = colours[7]; // G
- ResidueColour[8] = colours[10]; // H
- ResidueColour[9] = colours[0]; // I
- ResidueColour[10] = colours[0]; // L
- ResidueColour[11] = colours[4]; // K
- ResidueColour[12] = colours[0]; // M
- ResidueColour[13] = colours[0]; // F
- ResidueColour[14] = colours[8]; // P
- ResidueColour[15] = colours[1]; // S
- ResidueColour[16] = colours[1]; // T
- ResidueColour[17] = colours[0]; // W
- ResidueColour[18] = colours[10]; // Y
- ResidueColour[19] = colours[0]; // V
+ residueColour = new ConsensusColour[20];
+ residueColour[0] = colours[0]; // A
+ residueColour[1] = colours[4]; // R
+ residueColour[2] = colours[2]; // N
+ residueColour[3] = colours[6]; // D
+ residueColour[4] = colours[0]; // C
+ residueColour[5] = colours[3]; // Q
+ residueColour[6] = colours[5]; // E
+ residueColour[7] = colours[7]; // G
+ residueColour[8] = colours[10]; // H
+ residueColour[9] = colours[0]; // I
+ residueColour[10] = colours[0]; // L
+ residueColour[11] = colours[4]; // K
+ residueColour[12] = colours[0]; // M
+ residueColour[13] = colours[0]; // F
+ residueColour[14] = colours[8]; // P
+ residueColour[15] = colours[1]; // S
+ residueColour[16] = colours[1]; // T
+ residueColour[17] = colours[0]; // W
+ residueColour[18] = colours[10]; // Y
+ residueColour[19] = colours[0]; // V
}
+ @Override
public Color findColour(char c)
{
return Color.pink;
}
- public Color findColour(char c, int j)
+ @Override
+ protected Color findColour(char c, int j, SequenceI seq)
{
- Color currentColour;
-
- if (cons2.length <= j || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+ // TODO why the test for includeGaps here?
+ if (cons2.length <= j || Comparison.isGap(c)
+ /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
{
return Color.white;
}
int i = ResidueProperties.aaIndex[c];
- currentColour = Color.white;
+ Color colour = Color.white;
if (i > 19)
{
- return currentColour;
+ return colour;
}
- for (int k = 0; k < ResidueColour[i].conses.length; k++)
+ for (int k = 0; k < residueColour[i].cons.length; k++)
{
- if (ResidueColour[i].conses[k].isConserved(cons2, j, size, includeGaps))
+ if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
{
- currentColour = ResidueColour[i].c;
+ colour = residueColour[i].c;
}
}
if (i == 4)
{
+ /*
+ * override to colour C pink if >85% conserved
+ */
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
- currentColour = (Color) colhash.get("PINK");
+ colour = ClustalColour.PINK.colour;
}
}
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return colour;
}
/**
}
/**
- * @param includeGaps the includeGaps to set
+ * @param includeGaps
+ * the includeGaps to set
*/
protected void setIncludeGaps(boolean includeGaps)
{
this.includeGaps = includeGaps;
}
-}
-class ConsensusColour
-{
- Consensus[] conses;
- Color c;
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
+ {
+ ClustalxColourScheme css = new ClustalxColourScheme(sg,
+ view == null ? null : view.getHiddenRepSequences());
+ css.includeGaps = includeGaps;
+ return css;
+ }
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
- public ConsensusColour(Color c, Consensus[] conses)
+ @Override
+ public String getSchemeName()
{
- this.conses = conses;
+ return JalviewColourScheme.Clustal.toString();
+ }
- // this.list = list;
- this.c = c;
+ @Override
+ public boolean isSimple()
+ {
+ return false;
}
}
git://source.jalview.org / jalview.git / blobdiff