-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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
-public interface ColourSchemeI\r
-{\r
- public Color findColour(String aa);\r
-\r
- public Color findColour(String s, int j);\r
-\r
- public void setConsensus(java.util.Vector v);\r
-\r
- public void setConservation(jalview.analysis.Conservation c);\r
-\r
- public boolean conservationApplied();\r
-\r
- public void setConservationInc(int i);\r
-\r
- public int getConservationInc();\r
-\r
- public int getThreshold();\r
-\r
- public void setThreshold(int ct, boolean ignoreGaps);\r
-\r
-\r
-}\r
+/*
+ * 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.
+ *
+ * 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.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+
+public interface ColourSchemeI
+{
+ /**
+ * Returns the possibly context dependent colour for the given symbol at the
+ * aligned position in the given sequence. For example, the colour may depend
+ * on the symbol's relationship to the consensus residue for the column.
+ *
+ * @param symbol
+ * @param position
+ * @param seq
+ * @param consensusResidue
+ * the modal symbol (e.g. K) or symbols (e.g. KF) for the column
+ * @param pid
+ * the percentage identity of the column's consensus (if known)
+ * @return
+ */
+ Color findColour(char symbol, int position, SequenceI seq,
+ String consensusResidue, float pid);
+
+ /**
+ * Recalculate dependent data using the given sequence collection, taking
+ * account of hidden rows
+ *
+ * @param alignment
+ * @param hiddenReps
+ */
+ void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps);
+
+ /**
+ * Creates and returns a new instance of the colourscheme configured to colour
+ * the given collection. Note that even simple colour schemes should return a
+ * new instance for each call to this method, as different instances may have
+ * differing shading by consensus or percentage identity applied.
+ *
+ * @param viewport
+ * - the parent viewport
+ * @param sg
+ * - the collection of sequences to be coloured
+ * @return copy of current scheme with any inherited settings transferred
+ */
+ ColourSchemeI getInstance(AlignViewportI viewport,
+ AnnotatedCollectionI sg);
+
+ /**
+ * Answers true if the colour scheme is suitable for the given data, else
+ * false. For example, some colour schemes are specific to either peptide or
+ * nucleotide, or only apply if certain kinds of annotation are present.
+ *
+ * @param ac
+ * @return
+ */
+ // TODO can make this method static in Java 8
+ boolean isApplicableTo(AnnotatedCollectionI ac);
+
+ /**
+ * Answers the 'official' name of the colour scheme (as used, for example, as
+ * a Jalview startup parameter)
+ *
+ * @return
+ */
+ String getSchemeName();
+
+ /**
+ * Answers true if the colour scheme depends only on the sequence symbol, and
+ * not on other information such as alignment consensus or annotation. (Note
+ * that simple colour schemes may have a fading by percentage identity or
+ * conservation overlaid.) Simple colour schemes can be propagated to
+ * structure viewers.
+ *
+ * @return
+ */
+ boolean isSimple();
+
+ /**
+ * Answers true if the colour scheme has a colour specified for gaps.
+ *
+ * @return
+ */
+ boolean hasGapColour();
+}
git://source.jalview.org / jalview.git / blobdiff