X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=65c24c1ef6a8907624dea93705f3d89595bb8052;hb=9492f5b351797792472226ca975bb593653e8d94;hp=8deb556e23116b8009f91240cf332ebc023e5a01;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 8deb556..65c24c1 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,43 +1,98 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 java.awt.*;
+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);
- public Color findColour(char c, int j);
+ /**
+ *
+ * @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);
+ /**
+ *
+ * @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 hiddenReps);
+
}