-/*\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.util.*;\r
-\r
-import java.awt.*;\r
-\r
-public interface ColourSchemeI\r
-{\r
- public Color findColour(String aa);\r
-\r
- public Color findColour(String s, int j);\r
-\r
- public void setConsensus(Vector v);\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.
+ *
+ * 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 java.awt.Color;
+import java.util.Map;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+public interface ColourSchemeI
+{
+ /**
+ *
+ * @param c
+ * @return the colour for the given character
+ */
+ public Color findColour(char c);
+
+ /**
+ *
+ * @param c
+ * - sequence symbol or gap
+ * @param j
+ * - position in seq
+ * @param seq
+ * - sequence being coloured
+ * @return context dependent colour for the given symbol at the position in
+ * the given sequence
+ */
+ public Color findColour(char c, int j, SequenceI seq);
+
+ /**
+ * assign the given consensus profile for the colourscheme
+ */
+ public void setConsensus(java.util.Hashtable[] h);
+
+ /**
+ * assign the given conservation to the colourscheme
+ *
+ * @param c
+ */
+ public void setConservation(jalview.analysis.Conservation c);
+
+ /**
+ * enable or disable conservation shading for this colourscheme
+ *
+ * @param conservationApplied
+ */
+ public void setConservationApplied(boolean conservationApplied);
+
+ /**
+ *
+ * @return true if conservation shading is enabled for this colourscheme
+ */
+ public boolean conservationApplied();
+
+ /**
+ * set scale factor for bleaching of colour in unconserved regions
+ *
+ * @param i
+ */
+ public void setConservationInc(int i);
+
+ /**
+ *
+ * @return scale factor for bleaching colour in unconserved regions
+ */
+ public int getConservationInc();
+
+ /**
+ *
+ * @return percentage identity threshold for applying colourscheme
+ */
+ public int getThreshold();
+
+ /**
+ * set percentage identity threshold and type of %age identity calculation for
+ * shading
+ *
+ * @param ct
+ * 0..100 percentage identity for applying this colourscheme
+ * @param ignoreGaps
+ * when true, calculate PID without including gapped positions
+ */
+ public void setThreshold(int ct, boolean ignoreGaps);
+
+ /**
+ * recalculate dependent data using the given sequence collection, taking
+ * account of hidden rows
+ *
+ * @param alignment
+ * @param hiddenReps
+ */
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps);
+
+ /**
+ * create a new instance of the colourscheme configured to colour the given
+ * connection
+ *
+ * @param sg
+ * @param hiddenRepSequences
+ * @return copy of current scheme with any inherited settings transfered
+ */
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+
+}
git://source.jalview.org / jalview.git / blobdiff