X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;fp=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=6c8f40f9bf3ba9b9b5e1a1e1e854fa327dd7b74e;hb=fbc92d8f171f75002890bfa0ea1f436f7125d3b5;hp=850b1dcfb64f685c8e6d36514bf943a203d5fd8b;hpb=2fe4506613e52647dd9374151898ded61ea275df;p=jalview.git diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 850b1dc..6c8f40f 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -141,8 +141,7 @@ public class SequenceAnnotationReport void appendFeature(final StringBuilder sb, int rpos, Map minmax, SequenceFeature feature) { - String tmpString; - if (feature.getType().equals("disulfide bond")) + if (feature.isContactFeature()) { if (feature.getBegin() == rpos || feature.getEnd() == rpos) { @@ -150,7 +149,8 @@ public class SequenceAnnotationReport { sb.append("
"); } - sb.append("disulfide bond ").append(feature.getBegin()).append(":") + sb.append(feature.getType()).append(" ").append(feature.getBegin()) + .append(":") .append(feature.getEnd()); } } @@ -178,7 +178,7 @@ public class SequenceAnnotationReport if (feature.getDescription() != null && !feature.description.equals(feature.getType())) { - tmpString = feature.getDescription(); + String tmpString = feature.getDescription(); String tmp2up = tmpString.toUpperCase(); int startTag = tmp2up.indexOf(""); if (startTag > -1) @@ -223,11 +223,11 @@ public class SequenceAnnotationReport // check score should be shown if (!Float.isNaN(feature.getScore())) { - float[][] rng = (minmax == null) ? null : ((float[][]) minmax - .get(feature.getType())); + float[][] rng = (minmax == null) ? null : minmax.get(feature + .getType()); if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) { - sb.append(" Score=" + feature.getScore()); + sb.append(" Score=").append(String.valueOf(feature.getScore())); } } String status = (String) feature.getValue("status");