From 1595128a4bfc730f1e55c347f0a52eb0d491ca92 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 22 Jun 2020 12:19:02 +0100 Subject: [PATCH] JAL-3664 hmm related TODOs --- src/jalview/hmmer/HMMBuild.java | 1 + src/jalview/io/FileLoader.java | 1 + 2 files changed, 2 insertions(+) diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java index 0c47c1d..0bda090 100644 --- a/src/jalview/hmmer/HMMBuild.java +++ b/src/jalview/hmmer/HMMBuild.java @@ -201,6 +201,7 @@ public class HMMBuild extends HmmerCommand // at import level ? SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]); + // TODO: when copy contains the alignment sequences, you actually see the alignment sequences change to 'Sequence0'... if a redraw occurs! Hashtable sequencesHash = stashSequences(copyArray); exportStockholm(copyArray, alignmentFile, ac); diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 7061938..1126de6 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -441,6 +441,7 @@ public class FileLoader implements Runnable viewport.addAlignment(al, title); if (source instanceof HMMFile) { + // TODO: absorb into viewport.addAlignment above ? AlignmentI alignment = viewport.getAlignment(); SequenceI seq = alignment .getSequenceAt(alignment.getHeight() - 1); -- 1.7.10.2