- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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 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/>.
* 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/>.
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("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("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));
}
colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
}
- public ClustalxColourScheme(Vector seqs, int maxWidth)
+ public ClustalxColourScheme(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
- public void resetClustalX(Vector seqs, int maxWidth)
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
cons2 = new int[maxWidth][24];
includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
// get the current setting of the
cons2 = new int[maxWidth][24];
includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
// get the current setting of the
tmp6[0] = conses[3]; // -
tmp6[1] = conses[29]; // D
tmp6[2] = conses[10]; // E
tmp6[0] = conses[3]; // -
tmp6[1] = conses[29]; // D
tmp6[2] = conses[10]; // E
tmp6[4] = conses[19]; // Q
tmp6[5] = conses[2]; // DE
colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
tmp6[4] = conses[19]; // Q
tmp6[5] = conses[2]; // DE
colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ ClustalxColourScheme css= new ClustalxColourScheme(sg, hiddenRepSequences);
+ css.includeGaps = includeGaps;
+ return css;
+ }