X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=82e71b546fc42c5e991a2e902a86802ad5f49419;hb=3e88ca066c0cc12f1f1f4c63e9cd49e19586b2bd;hp=3336d47f6f136a2f6cdb170746460b544f6d61c1;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 3336d47..82e71b5 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -660,7 +660,7 @@ public class AnnotationFile String refSeqId = null; public boolean annotateAlignmentView(AlignViewportI viewport, - String file, String protocol) + String file, DataSourceType protocol) { ColumnSelection colSel = viewport.getColumnSelection(); if (colSel == null) @@ -678,31 +678,31 @@ public class AnnotationFile } public boolean readAnnotationFile(AlignmentI al, String file, - String protocol) + DataSourceType sourceType) { - return readAnnotationFile(al, null, file, protocol); + return readAnnotationFile(al, null, file, sourceType); } public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel, - String file, String protocol) + String file, DataSourceType sourceType) { BufferedReader in = null; try { - if (protocol.equals(AppletFormatAdapter.FILE)) + if (sourceType == DataSourceType.FILE) { in = new BufferedReader(new FileReader(file)); } - else if (protocol.equals(AppletFormatAdapter.URL)) + else if (sourceType == DataSourceType.URL) { URL url = new URL(file); in = new BufferedReader(new InputStreamReader(url.openStream())); } - else if (protocol.equals(AppletFormatAdapter.PASTE)) + else if (sourceType == DataSourceType.PASTE) { in = new BufferedReader(new StringReader(file)); } - else if (protocol.equals(AppletFormatAdapter.CLASSLOADER)) + else if (sourceType == DataSourceType.CLASSLOADER) { java.io.InputStream is = getClass().getResourceAsStream("/" + file); if (is != null) @@ -1637,9 +1637,8 @@ public class AnnotationFile else if (key.equalsIgnoreCase("consThreshold")) { sg.cs.setConservationInc(Integer.parseInt(value)); - Conservation c = new Conservation("Group", 3, - sg.getSequences(null), sg.getStartRes(), - sg.getEndRes() + 1); + Conservation c = new Conservation("Group", sg.getSequences(null), + sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); c.verdict(false, 25); // TODO: refer to conservation percent threshold