From 81d90a3969ade80091512d829a4fd2850d85b7bc Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Mon, 29 Aug 2005 15:51:52 +0000 Subject: [PATCH] Keep startRes the same after removing columns --- src/jalview/appletgui/AlignFrame.java | 15 +++++++++++++++ src/jalview/gui/AlignFrame.java | 16 ++++++++++++++++ 2 files changed, 31 insertions(+) diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 80e8438..dc8f72b 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -596,7 +596,16 @@ public class AlignFrame addHistoryItem(new HistoryItem("Remove Gapped Columns", viewport.alignment, HistoryItem.HIDE)); + + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + viewport.getAlignment().removeGaps(); + + viewport.setStartRes(seq.findIndex(startRes)-1); + viewport.updateConservation(); viewport.updateConsensus(); resetAllClustalSchemes(); @@ -608,6 +617,11 @@ public class AlignFrame addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, HistoryItem.HIDE)); + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + SequenceI current; int jSize; @@ -645,6 +659,7 @@ public class AlignFrame while(j < end && j < jSize) ; } + viewport.setStartRes(seq.findIndex(startRes)-1); resetAllClustalSchemes(); viewport.updateConservation(); viewport.updateConsensus(); diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 084ad7d..bdca06c 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -960,7 +960,15 @@ public class AlignFrame addHistoryItem(new HistoryItem("Remove Gapped Columns", viewport.alignment, HistoryItem.HIDE)); + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + viewport.getAlignment().removeGaps(); + + viewport.setStartRes(seq.findIndex(startRes)-1); + resetAllClustalSchemes(); viewport.updateConservation(); viewport.updateConsensus(); @@ -977,6 +985,12 @@ public class AlignFrame addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, HistoryItem.HIDE)); + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + + SequenceI current; int jSize; @@ -1018,6 +1032,8 @@ public class AlignFrame while (j < end && j < jSize); } + viewport.setStartRes(seq.findIndex(startRes)-1); + resetAllClustalSchemes(); viewport.updateConservation(); -- 1.7.10.2