+/*
+ * 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.
+ */
// Requested by David M Garcia (v3)
// very messy script to output the scores in annotation rows
// for the first sequence in a selection on the topmost alignment
import static java.awt.Toolkit.*
-def curviewport = Jalview.getAlignframes()[Jalview.getAlignframes().length-1].getViewport();
+def curviewport = Jalview.getAlignFrames()[Jalview.getAlignFrames().length-1].getViewport();
// TSV output by default.
// change "\t" to "," to output CSV file
String csv=""
gaps.eachWithIndex{col,spos -> if (col>=selreg.getStartRes() && col<=selreg.getEndRes()) {
// add sequence for debugging
- if (count>sseq.length()) { sseq+=sep+selreg.getSequenceAt(0).getCharAt(col); count=sseq.length()+1;};
+ if (count>sseq.length()) {
+ sseq+=sep+selreg.getSequenceAt(0).getCharAt(col); count=sseq.length()+1;
+ };
// output height of histogram
- csv+=sep+aa.annotations[col].value;
+ csv+=sep;
+ def annot = aa.annotations[col];
+ if (annot != null) {
+ csv+=aa.annotations[col].value;
+ }
// Uncomment to output string shown in tooltip
// csv+=sep+aa.annotations[col].description;
}}