From 99c58ee0ae2a848f982552e53feaf6d5cb9925e5 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 8 Jun 2005 13:14:54 +0000 Subject: [PATCH] GPL license added --- src/MCview/Atom.java | 19 + src/MCview/Bond.java | 19 + src/MCview/MCMatrix.java | 19 + src/MCview/PDBChain.java | 35 +- src/MCview/PDBfile.java | 19 + src/MCview/Residue.java | 19 + src/MCview/Zsort.java | 19 + src/MCview/myAtom.java | 19 + src/MCview/rotCanvas.java | 19 + src/ext/vamsas/JPredWS.java | 19 + src/ext/vamsas/JPredWSService.java | 19 + src/ext/vamsas/JPredWSServiceLocator.java | 19 + src/ext/vamsas/JpredResult.java | 45 +- src/ext/vamsas/JpredSoapBindingStub.java | 19 + src/ext/vamsas/Msfalignment.java | 45 +- src/ext/vamsas/MuscleWS.java | 19 + src/ext/vamsas/MuscleWSService.java | 19 + src/ext/vamsas/MuscleWSServiceLocator.java | 19 + src/ext/vamsas/MuscleWSSoapBindingStub.java | 19 + src/ext/vamsas/Result.java | 79 +-- src/ext/vamsas/Secstructpred.java | 39 +- src/ext/vamsas/Sequence.java | 45 +- src/jalview/analysis/AAFrequency.java | 19 + src/jalview/analysis/AlignSeq.java | 36 +- src/jalview/analysis/AlignmentSorter.java | 28 +- src/jalview/analysis/AlignmentUtil.java | 19 + src/jalview/analysis/CompareAlignments.java | 19 + src/jalview/analysis/Conservation.java | 36 +- src/jalview/analysis/NJTree.java | 19 + src/jalview/analysis/PCA.java | 20 +- src/jalview/analysis/SeqsetUtils.java | 19 + src/jalview/analysis/SequenceIdMatcher.java | 19 + src/jalview/appletgui/APopupMenu.java | 19 + src/jalview/appletgui/AlignFrame.java | 28 +- src/jalview/appletgui/AlignViewport.java | 19 + src/jalview/appletgui/AlignmentPanel.java | 19 + src/jalview/appletgui/AnnotationLabels.java | 19 + src/jalview/appletgui/AnnotationPanel.java | 19 + src/jalview/appletgui/ColumnSelection.java | 19 + src/jalview/appletgui/CutAndPasteTransfer.java | 25 +- src/jalview/appletgui/FeatureRenderer.java | 19 + src/jalview/appletgui/Finder.java | 19 + src/jalview/appletgui/FontChooser.java | 19 + src/jalview/appletgui/IdCanvas.java | 19 + src/jalview/appletgui/IdPanel.java | 19 + src/jalview/appletgui/IdwidthAdjuster.java | 19 + src/jalview/appletgui/OverviewPanel.java | 19 + src/jalview/appletgui/PCAPanel.java | 19 + src/jalview/appletgui/PaintRefresher.java | 19 + src/jalview/appletgui/PairwiseAlignPanel.java | 19 + src/jalview/appletgui/RedundancyPanel.java | 19 + src/jalview/appletgui/RotatableCanvas.java | 19 + src/jalview/appletgui/ScalePanel.java | 19 + src/jalview/appletgui/SeqCanvas.java | 19 + src/jalview/appletgui/SeqPanel.java | 19 + src/jalview/appletgui/SequenceRenderer.java | 19 + src/jalview/appletgui/SliderPanel.java | 19 + src/jalview/appletgui/TreeCanvas.java | 19 + src/jalview/appletgui/TreePanel.java | 19 + src/jalview/appletgui/UserDefinedColours.java | 19 + src/jalview/bin/Cache.java | 26 +- src/jalview/bin/Jalview.java | 26 +- src/jalview/bin/JalviewLite.java | 19 + src/jalview/binding/Alignment.java | 79 +-- src/jalview/binding/Annotation.java | 177 ++++--- src/jalview/binding/AnnotationElement.java | 127 +++-- src/jalview/binding/Colour.java | 79 +-- src/jalview/binding/JGroup.java | 317 +++++------ src/jalview/binding/JSeq.java | 143 ++--- src/jalview/binding/JalviewModel.java | 87 ++-- src/jalview/binding/JalviewModelSequence.java | 375 +++++++------- src/jalview/binding/JalviewModelSequence2.java | 141 ++--- src/jalview/binding/JalviewModelSequence2Item.java | 101 ++-- src/jalview/binding/JalviewUserColours.java | 141 ++--- src/jalview/binding/JalviewUserColoursItem.java | 31 +- src/jalview/binding/Residue.java | 91 ++-- src/jalview/binding/Sequence.java | 65 ++- src/jalview/binding/SequenceSet.java | 247 +++++---- src/jalview/binding/SequenceType.java | 87 ++-- src/jalview/binding/UserColour.java | 91 ++-- src/jalview/binding/UserColourScheme.java | 65 ++- src/jalview/binding/UserColours.java | 79 +-- src/jalview/binding/VAMSAS.java | 297 ++++++----- src/jalview/binding/VamsasModel.java | 65 ++- src/jalview/binding/Viewport.java | 548 ++++++++++---------- src/jalview/datamodel/Alignment.java | 19 + src/jalview/datamodel/AlignmentAnnotation.java | 19 + src/jalview/datamodel/AlignmentI.java | 19 + src/jalview/datamodel/AlignmentOrder.java | 19 + src/jalview/datamodel/Annotation.java | 19 + src/jalview/datamodel/BinaryNode.java | 19 + src/jalview/datamodel/BinarySequence.java | 36 +- src/jalview/datamodel/HistoryItem.java | 19 + src/jalview/datamodel/Sequence.java | 19 + src/jalview/datamodel/SequenceFeature.java | 19 + src/jalview/datamodel/SequenceGroup.java | 19 + src/jalview/datamodel/SequenceI.java | 19 + src/jalview/datamodel/SequenceNode.java | 19 + src/jalview/datamodel/SequencePoint.java | 35 +- src/jalview/datamodel/SuperGroup.java | 19 + src/jalview/gui/AlignFrame.java | 30 +- src/jalview/gui/AlignViewport.java | 19 + src/jalview/gui/AlignmentPanel.java | 19 + src/jalview/gui/AnnotationLabels.java | 19 + src/jalview/gui/AnnotationPanel.java | 19 + src/jalview/gui/ColumnSelection.java | 19 + src/jalview/gui/CutAndPasteTransfer.java | 25 +- src/jalview/gui/Desktop.java | 26 +- src/jalview/gui/FeatureRenderer.java | 19 + src/jalview/gui/Finder.java | 19 + src/jalview/gui/FontChooser.java | 19 + src/jalview/gui/IdCanvas.java | 19 + src/jalview/gui/IdPanel.java | 19 + src/jalview/gui/IdwidthAdjuster.java | 19 + src/jalview/gui/Jalview2XML.java | 27 + src/jalview/gui/OverviewPanel.java | 19 + src/jalview/gui/PCAPanel.java | 19 + src/jalview/gui/PaintRefresher.java | 19 + src/jalview/gui/PairwiseAlignPanel.java | 19 + src/jalview/gui/PopupMenu.java | 19 + src/jalview/gui/Preferences.java | 19 + src/jalview/gui/RedundancyPanel.java | 19 + src/jalview/gui/RotatableCanvas.java | 19 + src/jalview/gui/ScalePanel.java | 19 + src/jalview/gui/SeqCanvas.java | 19 + src/jalview/gui/SeqPanel.java | 19 + src/jalview/gui/SequenceRenderer.java | 19 + src/jalview/gui/SliderPanel.java | 19 + src/jalview/gui/SplashScreen.java | 19 + src/jalview/gui/TreeCanvas.java | 19 + src/jalview/gui/TreePanel.java | 19 + src/jalview/gui/UserDefinedColours.java | 19 + src/jalview/gui/WebserviceInfo.java | 19 + src/jalview/io/AlignFile.java | 19 + src/jalview/io/BLCFile.java | 36 +- src/jalview/io/ClustalFile.java | 19 + src/jalview/io/EBIFetchClient.java | 19 + src/jalview/io/FastaFile.java | 19 + src/jalview/io/FileParse.java | 19 + src/jalview/io/FormatAdapter.java | 19 + src/jalview/io/HTMLOutput.java | 19 + src/jalview/io/IdentifyFile.java | 25 +- src/jalview/io/JPredFile.java | 20 + src/jalview/io/JalviewFileChooser.java | 19 + src/jalview/io/JalviewFileFilter.java | 19 + src/jalview/io/JalviewFileView.java | 19 + src/jalview/io/MSFfile.java | 19 + src/jalview/io/NewickFile.java | 20 + src/jalview/io/PIRFile.java | 36 +- src/jalview/io/PfamFile.java | 19 + src/jalview/io/PileUpfile.java | 19 + src/jalview/io/SequenceFeatureFetcher.java | 19 + src/jalview/io/WSWUBlastClient.java | 19 + src/jalview/jbappletgui/GAlignFrame.java | 25 +- src/jalview/jbappletgui/GAlignmentPanel.java | 25 +- src/jalview/jbappletgui/GCutAndPasteTransfer.java | 25 +- src/jalview/jbappletgui/GFinder.java | 19 + src/jalview/jbappletgui/GFontChooser.java | 19 + src/jalview/jbappletgui/GPCAPanel.java | 19 + src/jalview/jbappletgui/GPairwiseAlignPanel.java | 19 + src/jalview/jbappletgui/GSliderPanel.java | 19 + src/jalview/jbappletgui/GTreePanel.java | 19 + src/jalview/jbappletgui/GUserDefinedColours.java | 19 + src/jalview/jbgui/GAlignFrame.java | 25 +- src/jalview/jbgui/GAlignmentPanel.java | 25 +- src/jalview/jbgui/GCutAndPasteTransfer.java | 25 +- src/jalview/jbgui/GDesktop.java | 25 +- src/jalview/jbgui/GFinder.java | 19 + src/jalview/jbgui/GFontChooser.java | 19 + src/jalview/jbgui/GPCAPanel.java | 19 + src/jalview/jbgui/GPairwiseAlignPanel.java | 19 + src/jalview/jbgui/GPreferences.java | 19 + src/jalview/jbgui/GSliderPanel.java | 19 + src/jalview/jbgui/GTreePanel.java | 19 + src/jalview/jbgui/GUserDefinedColours.java | 19 + src/jalview/jbgui/GWebserviceInfo.java | 19 + src/jalview/math/Matrix.java | 19 + src/jalview/math/RotatableMatrix.java | 19 + src/jalview/schemes/Blosum62ColourScheme.java | 35 +- src/jalview/schemes/BuriedColourScheme.java | 19 + src/jalview/schemes/ClustalxColourScheme.java | 35 +- src/jalview/schemes/ColourSchemeI.java | 19 + src/jalview/schemes/ColourSchemeProperty.java | 19 + src/jalview/schemes/Consensus.java | 35 +- src/jalview/schemes/ConservationColourScheme.java | 35 +- src/jalview/schemes/HelixColourScheme.java | 35 +- src/jalview/schemes/HydrophobicColourScheme.java | 35 +- src/jalview/schemes/NucleotideColourScheme.java | 19 + src/jalview/schemes/PIDColourScheme.java | 19 + src/jalview/schemes/ResidueColourScheme.java | 19 + src/jalview/schemes/ResidueProperties.java | 8 +- src/jalview/schemes/ScoreColourScheme.java | 19 + src/jalview/schemes/StrandColourScheme.java | 36 +- src/jalview/schemes/TaylorColourScheme.java | 19 + src/jalview/schemes/TurnColourScheme.java | 35 +- src/jalview/schemes/UserColourScheme.java | 35 +- src/jalview/schemes/ZappoColourScheme.java | 19 + src/jalview/util/BrowserLauncher.java | 25 +- src/jalview/util/Comparison.java | 19 + src/jalview/util/Format.java | 1 + src/jalview/util/QuickSort.java | 19 + src/jalview/ws/JPredClient.java | 19 + src/jalview/ws/MsaWSClient.java | 19 + src/jalview/ws/MsaWServices.java | 19 + src/jalview/ws/WSClient.java | 19 + src/jalview/ws/WSClientI.java | 19 + src/vamsas/IMsaWS.java | 23 +- src/vamsas/objects/simple/Alignment.java | 39 +- src/vamsas/objects/simple/Alignment_Helper.java | 31 +- src/vamsas/objects/simple/MsaResult.java | 27 +- src/vamsas/objects/simple/MsaResult_Helper.java | 31 +- src/vamsas/objects/simple/Object.java | 19 + src/vamsas/objects/simple/Object_Helper.java | 31 +- src/vamsas/objects/simple/Result.java | 67 ++- src/vamsas/objects/simple/Result_Helper.java | 31 +- src/vamsas/objects/simple/Sequence.java | 33 +- src/vamsas/objects/simple/SequenceSet.java | 27 +- src/vamsas/objects/simple/SequenceSet_Helper.java | 31 +- src/vamsas/objects/simple/Sequence_Helper.java | 31 +- src/vamsas/objects/simple/WsJobId.java | 31 +- src/vamsas/objects/simple/WsJobId_Helper.java | 31 +- 221 files changed, 5836 insertions(+), 2094 deletions(-) diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java index c89d489..b3a8fdb 100755 --- a/src/MCview/Atom.java +++ b/src/MCview/Atom.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package MCview; import java.util.*; import java.awt.*; diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java index 60b2f21..c84152a 100755 --- a/src/MCview/Bond.java +++ b/src/MCview/Bond.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package MCview; import java.awt.*; diff --git a/src/MCview/MCMatrix.java b/src/MCview/MCMatrix.java index 4994573..31af9d4 100755 --- a/src/MCview/MCMatrix.java +++ b/src/MCview/MCMatrix.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package MCview; public class MCMatrix { diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 2e0ce30..fdb74bd 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -1,19 +1,22 @@ -/* Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package MCview; import jalview.datamodel.*; diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 44bf1bc..1937a8f 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package MCview; import jalview.datamodel.*; diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java index 6e058f3..998e388 100755 --- a/src/MCview/Residue.java +++ b/src/MCview/Residue.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package MCview; import java.util.*; diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java index 4116ff3..215f753 100755 --- a/src/MCview/Zsort.java +++ b/src/MCview/Zsort.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package MCview; import java.util.*; diff --git a/src/MCview/myAtom.java b/src/MCview/myAtom.java index 93166a5..27a4b08 100755 --- a/src/MCview/myAtom.java +++ b/src/MCview/myAtom.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package MCview; import java.util.*; diff --git a/src/MCview/rotCanvas.java b/src/MCview/rotCanvas.java index eb5fd64..a165129 100755 --- a/src/MCview/rotCanvas.java +++ b/src/MCview/rotCanvas.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package MCview; // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug import java.awt.*; diff --git a/src/ext/vamsas/JPredWS.java b/src/ext/vamsas/JPredWS.java index 801bf86..82e58c2 100755 --- a/src/ext/vamsas/JPredWS.java +++ b/src/ext/vamsas/JPredWS.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public interface JPredWS extends java.rmi.Remote { diff --git a/src/ext/vamsas/JPredWSService.java b/src/ext/vamsas/JPredWSService.java index e1f8cbe..e14c51d 100755 --- a/src/ext/vamsas/JPredWSService.java +++ b/src/ext/vamsas/JPredWSService.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public interface JPredWSService extends javax.xml.rpc.Service { diff --git a/src/ext/vamsas/JPredWSServiceLocator.java b/src/ext/vamsas/JPredWSServiceLocator.java index 0faea4c..af51043 100755 --- a/src/ext/vamsas/JPredWSServiceLocator.java +++ b/src/ext/vamsas/JPredWSServiceLocator.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public class JPredWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.JPredWSService { diff --git a/src/ext/vamsas/JpredResult.java b/src/ext/vamsas/JpredResult.java index d798def..741d3df 100755 --- a/src/ext/vamsas/JpredResult.java +++ b/src/ext/vamsas/JpredResult.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public class JpredResult extends ext.vamsas.Result implements java.io.Serializable { @@ -24,7 +43,7 @@ public class JpredResult extends ext.vamsas.Result implements java.io.Serializ /** * Gets the aligfile value for this JpredResult. - * + * * @return aligfile */ public java.lang.String getAligfile() { @@ -34,7 +53,7 @@ public class JpredResult extends ext.vamsas.Result implements java.io.Serializ /** * Sets the aligfile value for this JpredResult. - * + * * @param aligfile */ public void setAligfile(java.lang.String aligfile) { @@ -44,7 +63,7 @@ public class JpredResult extends ext.vamsas.Result implements java.io.Serializ /** * Gets the predfile value for this JpredResult. - * + * * @return predfile */ public java.lang.String getPredfile() { @@ -54,7 +73,7 @@ public class JpredResult extends ext.vamsas.Result implements java.io.Serializ /** * Sets the predfile value for this JpredResult. - * + * * @param predfile */ public void setPredfile(java.lang.String predfile) { @@ -72,11 +91,11 @@ public class JpredResult extends ext.vamsas.Result implements java.io.Serializ } __equalsCalc = obj; boolean _equals; - _equals = super.equals(obj) && - ((this.aligfile==null && other.getAligfile()==null) || + _equals = super.equals(obj) && + ((this.aligfile==null && other.getAligfile()==null) || (this.aligfile!=null && this.aligfile.equals(other.getAligfile()))) && - ((this.predfile==null && other.getPredfile()==null) || + ((this.predfile==null && other.getPredfile()==null) || (this.predfile!=null && this.predfile.equals(other.getPredfile()))); __equalsCalc = null; @@ -129,10 +148,10 @@ public class JpredResult extends ext.vamsas.Result implements java.io.Serializ * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -141,10 +160,10 @@ public class JpredResult extends ext.vamsas.Result implements java.io.Serializ * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java index f11fbe3..d27a582 100755 --- a/src/ext/vamsas/JpredSoapBindingStub.java +++ b/src/ext/vamsas/JpredSoapBindingStub.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements ext.vamsas.JPredWS { diff --git a/src/ext/vamsas/Msfalignment.java b/src/ext/vamsas/Msfalignment.java index 70ed612..d94e2b9 100755 --- a/src/ext/vamsas/Msfalignment.java +++ b/src/ext/vamsas/Msfalignment.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public class Msfalignment implements java.io.Serializable { @@ -24,7 +43,7 @@ public class Msfalignment implements java.io.Serializable { /** * Gets the msf value for this Msfalignment. - * + * * @return msf */ public java.lang.String getMsf() { @@ -34,7 +53,7 @@ public class Msfalignment implements java.io.Serializable { /** * Sets the msf value for this Msfalignment. - * + * * @param msf */ public void setMsf(java.lang.String msf) { @@ -44,7 +63,7 @@ public class Msfalignment implements java.io.Serializable { /** * Gets the notes value for this Msfalignment. - * + * * @return notes */ public java.lang.String getNotes() { @@ -54,7 +73,7 @@ public class Msfalignment implements java.io.Serializable { /** * Sets the notes value for this Msfalignment. - * + * * @param notes */ public void setNotes(java.lang.String notes) { @@ -72,11 +91,11 @@ public class Msfalignment implements java.io.Serializable { } __equalsCalc = obj; boolean _equals; - _equals = true && - ((this.msf==null && other.getMsf()==null) || + _equals = true && + ((this.msf==null && other.getMsf()==null) || (this.msf!=null && this.msf.equals(other.getMsf()))) && - ((this.notes==null && other.getNotes()==null) || + ((this.notes==null && other.getNotes()==null) || (this.notes!=null && this.notes.equals(other.getNotes()))); __equalsCalc = null; @@ -129,10 +148,10 @@ public class Msfalignment implements java.io.Serializable { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -141,10 +160,10 @@ public class Msfalignment implements java.io.Serializable { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/ext/vamsas/MuscleWS.java b/src/ext/vamsas/MuscleWS.java index 26e1f83..37f851d 100755 --- a/src/ext/vamsas/MuscleWS.java +++ b/src/ext/vamsas/MuscleWS.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public interface MuscleWS extends java.rmi.Remote { diff --git a/src/ext/vamsas/MuscleWSService.java b/src/ext/vamsas/MuscleWSService.java index 04026a3..b1a41cc 100755 --- a/src/ext/vamsas/MuscleWSService.java +++ b/src/ext/vamsas/MuscleWSService.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public interface MuscleWSService extends javax.xml.rpc.Service { diff --git a/src/ext/vamsas/MuscleWSServiceLocator.java b/src/ext/vamsas/MuscleWSServiceLocator.java index 03f10d0..fd906cd 100755 --- a/src/ext/vamsas/MuscleWSServiceLocator.java +++ b/src/ext/vamsas/MuscleWSServiceLocator.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public class MuscleWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.MuscleWSService { diff --git a/src/ext/vamsas/MuscleWSSoapBindingStub.java b/src/ext/vamsas/MuscleWSSoapBindingStub.java index 52914a5..b2739bd 100755 --- a/src/ext/vamsas/MuscleWSSoapBindingStub.java +++ b/src/ext/vamsas/MuscleWSSoapBindingStub.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub implements ext.vamsas.MuscleWS { diff --git a/src/ext/vamsas/Result.java b/src/ext/vamsas/Result.java index a2da004..97d766b 100755 --- a/src/ext/vamsas/Result.java +++ b/src/ext/vamsas/Result.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public class Result implements java.io.Serializable { @@ -51,7 +70,7 @@ public class Result implements java.io.Serializable { /** * Gets the broken value for this Result. - * + * * @return broken */ public boolean isBroken() { @@ -61,7 +80,7 @@ public class Result implements java.io.Serializable { /** * Sets the broken value for this Result. - * + * * @param broken */ public void setBroken(boolean broken) { @@ -71,7 +90,7 @@ public class Result implements java.io.Serializable { /** * Gets the failed value for this Result. - * + * * @return failed */ public boolean isFailed() { @@ -81,7 +100,7 @@ public class Result implements java.io.Serializable { /** * Sets the failed value for this Result. - * + * * @param failed */ public void setFailed(boolean failed) { @@ -91,7 +110,7 @@ public class Result implements java.io.Serializable { /** * Gets the finished value for this Result. - * + * * @return finished */ public boolean isFinished() { @@ -101,7 +120,7 @@ public class Result implements java.io.Serializable { /** * Sets the finished value for this Result. - * + * * @param finished */ public void setFinished(boolean finished) { @@ -111,7 +130,7 @@ public class Result implements java.io.Serializable { /** * Gets the invalid value for this Result. - * + * * @return invalid */ public boolean isInvalid() { @@ -121,7 +140,7 @@ public class Result implements java.io.Serializable { /** * Sets the invalid value for this Result. - * + * * @param invalid */ public void setInvalid(boolean invalid) { @@ -131,7 +150,7 @@ public class Result implements java.io.Serializable { /** * Gets the jobFailed value for this Result. - * + * * @return jobFailed */ public boolean isJobFailed() { @@ -141,7 +160,7 @@ public class Result implements java.io.Serializable { /** * Sets the jobFailed value for this Result. - * + * * @param jobFailed */ public void setJobFailed(boolean jobFailed) { @@ -151,7 +170,7 @@ public class Result implements java.io.Serializable { /** * Gets the queued value for this Result. - * + * * @return queued */ public boolean isQueued() { @@ -161,7 +180,7 @@ public class Result implements java.io.Serializable { /** * Sets the queued value for this Result. - * + * * @param queued */ public void setQueued(boolean queued) { @@ -171,7 +190,7 @@ public class Result implements java.io.Serializable { /** * Gets the running value for this Result. - * + * * @return running */ public boolean isRunning() { @@ -181,7 +200,7 @@ public class Result implements java.io.Serializable { /** * Sets the running value for this Result. - * + * * @param running */ public void setRunning(boolean running) { @@ -191,7 +210,7 @@ public class Result implements java.io.Serializable { /** * Gets the serverError value for this Result. - * + * * @return serverError */ public boolean isServerError() { @@ -201,7 +220,7 @@ public class Result implements java.io.Serializable { /** * Sets the serverError value for this Result. - * + * * @param serverError */ public void setServerError(boolean serverError) { @@ -211,7 +230,7 @@ public class Result implements java.io.Serializable { /** * Gets the state value for this Result. - * + * * @return state */ public int getState() { @@ -221,7 +240,7 @@ public class Result implements java.io.Serializable { /** * Sets the state value for this Result. - * + * * @param state */ public void setState(int state) { @@ -231,7 +250,7 @@ public class Result implements java.io.Serializable { /** * Gets the status value for this Result. - * + * * @return status */ public java.lang.String getStatus() { @@ -241,7 +260,7 @@ public class Result implements java.io.Serializable { /** * Sets the status value for this Result. - * + * * @param status */ public void setStatus(java.lang.String status) { @@ -251,7 +270,7 @@ public class Result implements java.io.Serializable { /** * Gets the suspended value for this Result. - * + * * @return suspended */ public boolean isSuspended() { @@ -261,7 +280,7 @@ public class Result implements java.io.Serializable { /** * Sets the suspended value for this Result. - * + * * @param suspended */ public void setSuspended(boolean suspended) { @@ -279,7 +298,7 @@ public class Result implements java.io.Serializable { } __equalsCalc = obj; boolean _equals; - _equals = true && + _equals = true && this.broken == other.isBroken() && this.failed == other.isFailed() && this.finished == other.isFinished() && @@ -289,7 +308,7 @@ public class Result implements java.io.Serializable { this.running == other.isRunning() && this.serverError == other.isServerError() && this.state == other.getState() && - ((this.status==null && other.getStatus()==null) || + ((this.status==null && other.getStatus()==null) || (this.status!=null && this.status.equals(other.getStatus()))) && this.suspended == other.isSuspended(); @@ -395,10 +414,10 @@ public class Result implements java.io.Serializable { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -407,10 +426,10 @@ public class Result implements java.io.Serializable { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/ext/vamsas/Secstructpred.java b/src/ext/vamsas/Secstructpred.java index 777b41f..290ac3c 100755 --- a/src/ext/vamsas/Secstructpred.java +++ b/src/ext/vamsas/Secstructpred.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public class Secstructpred implements java.io.Serializable { @@ -21,7 +40,7 @@ public class Secstructpred implements java.io.Serializable { /** * Gets the output value for this Secstructpred. - * + * * @return output */ public java.lang.String getOutput() { @@ -31,7 +50,7 @@ public class Secstructpred implements java.io.Serializable { /** * Sets the output value for this Secstructpred. - * + * * @param output */ public void setOutput(java.lang.String output) { @@ -49,8 +68,8 @@ public class Secstructpred implements java.io.Serializable { } __equalsCalc = obj; boolean _equals; - _equals = true && - ((this.output==null && other.getOutput()==null) || + _equals = true && + ((this.output==null && other.getOutput()==null) || (this.output!=null && this.output.equals(other.getOutput()))); __equalsCalc = null; @@ -95,10 +114,10 @@ public class Secstructpred implements java.io.Serializable { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -107,10 +126,10 @@ public class Secstructpred implements java.io.Serializable { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/ext/vamsas/Sequence.java b/src/ext/vamsas/Sequence.java index 7d2d730..c2b9da8 100755 --- a/src/ext/vamsas/Sequence.java +++ b/src/ext/vamsas/Sequence.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package ext.vamsas; public class Sequence implements java.io.Serializable { @@ -24,7 +43,7 @@ public class Sequence implements java.io.Serializable { /** * Gets the id value for this Sequence. - * + * * @return id */ public java.lang.String getId() { @@ -34,7 +53,7 @@ public class Sequence implements java.io.Serializable { /** * Sets the id value for this Sequence. - * + * * @param id */ public void setId(java.lang.String id) { @@ -44,7 +63,7 @@ public class Sequence implements java.io.Serializable { /** * Gets the seq value for this Sequence. - * + * * @return seq */ public java.lang.String getSeq() { @@ -54,7 +73,7 @@ public class Sequence implements java.io.Serializable { /** * Sets the seq value for this Sequence. - * + * * @param seq */ public void setSeq(java.lang.String seq) { @@ -72,11 +91,11 @@ public class Sequence implements java.io.Serializable { } __equalsCalc = obj; boolean _equals; - _equals = true && - ((this.id==null && other.getId()==null) || + _equals = true && + ((this.id==null && other.getId()==null) || (this.id!=null && this.id.equals(other.getId()))) && - ((this.seq==null && other.getSeq()==null) || + ((this.seq==null && other.getSeq()==null) || (this.seq!=null && this.seq.equals(other.getSeq()))); __equalsCalc = null; @@ -129,10 +148,10 @@ public class Sequence implements java.io.Serializable { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -141,10 +160,10 @@ public class Sequence implements java.io.Serializable { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index edcc50f..02569ef 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.analysis; import jalview.jbgui.*; diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index 4f36c57..e77a0d3 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -1,20 +1,22 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.analysis; import jalview.schemes.*; diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index 8274768..53eb1dd 100755 --- a/src/jalview/analysis/AlignmentSorter.java +++ b/src/jalview/analysis/AlignmentSorter.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.analysis; import jalview.datamodel.*; @@ -35,13 +54,7 @@ public class AlignmentSorter { QuickSort.sort(arr,s); - Vector newg = new Vector(nGroup); - - for (int i=nGroup-1; i >= 0; i--) { - newg.addElement(s[i]); - } - - // align.setGroups(newg); + // align..setGroups(newg); } /** @@ -122,7 +135,6 @@ public class AlignmentSorter { static boolean sortGroupAscending = true; public static void sortByGroup(AlignmentI align) { - int nSeq = align.getHeight(); Vector groups = align.getGroups(); if (groups.hashCode()!=lastGroupHash) { sortGroupAscending=true; diff --git a/src/jalview/analysis/AlignmentUtil.java b/src/jalview/analysis/AlignmentUtil.java index 2192866..b992f4a 100755 --- a/src/jalview/analysis/AlignmentUtil.java +++ b/src/jalview/analysis/AlignmentUtil.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.analysis; import jalview.datamodel.*; diff --git a/src/jalview/analysis/CompareAlignments.java b/src/jalview/analysis/CompareAlignments.java index 3cb8144..e2dd742 100755 --- a/src/jalview/analysis/CompareAlignments.java +++ b/src/jalview/analysis/CompareAlignments.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.analysis; import jalview.datamodel.*; diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index deeb2e9..d3f1e01 100755 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -1,20 +1,22 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.analysis; diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java index 85749a1..75d36c1 100755 --- a/src/jalview/analysis/NJTree.java +++ b/src/jalview/analysis/NJTree.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.analysis; import jalview.datamodel.*; diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java index 0d998b5..3948695 100755 --- a/src/jalview/analysis/PCA.java +++ b/src/jalview/analysis/PCA.java @@ -1,4 +1,22 @@ -// PCA.java +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.analysis; import jalview.math.*; diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java index 98b1902..faa08e1 100755 --- a/src/jalview/analysis/SeqsetUtils.java +++ b/src/jalview/analysis/SeqsetUtils.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.analysis; import jalview.datamodel.SequenceI; diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java index b620205..1c156cd 100755 --- a/src/jalview/analysis/SequenceIdMatcher.java +++ b/src/jalview/analysis/SequenceIdMatcher.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.analysis; import java.util.Vector; diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index a932d66..42643d0 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.datamodel.*; diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 5b0aae2..7d0c985 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,13 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *****************a**/ - - - +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.appletgui; diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index a00b318..bdc2359 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import java.awt.*; diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 0075862..9c77e13 100755 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.jbappletgui.GAlignmentPanel; diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index 57aeb06..095377d 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -1,4 +1,23 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import java.awt.event.*; diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index 2cf5beb..afdc6db 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.datamodel.*; diff --git a/src/jalview/appletgui/ColumnSelection.java b/src/jalview/appletgui/ColumnSelection.java index 4ec546a..cb83c4a 100755 --- a/src/jalview/appletgui/ColumnSelection.java +++ b/src/jalview/appletgui/ColumnSelection.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import java.util.*; diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java index b774cdf..22cfd67 100755 --- a/src/jalview/appletgui/CutAndPasteTransfer.java +++ b/src/jalview/appletgui/CutAndPasteTransfer.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.appletgui; diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index a8412f0..f6fe0be 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.datamodel.*; diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java index 58670d8..e6fb5e6 100755 --- a/src/jalview/appletgui/Finder.java +++ b/src/jalview/appletgui/Finder.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.jbappletgui.GFinder; diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java index db0c16f..eb29211 100755 --- a/src/jalview/appletgui/FontChooser.java +++ b/src/jalview/appletgui/FontChooser.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.jbappletgui.GFontChooser; diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java index a8f8456..5b7aa1e 100755 --- a/src/jalview/appletgui/IdCanvas.java +++ b/src/jalview/appletgui/IdCanvas.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import java.awt.*; diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index b6a5b47..4998360 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import java.awt.*; diff --git a/src/jalview/appletgui/IdwidthAdjuster.java b/src/jalview/appletgui/IdwidthAdjuster.java index e748697..5e5df30 100755 --- a/src/jalview/appletgui/IdwidthAdjuster.java +++ b/src/jalview/appletgui/IdwidthAdjuster.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import java.awt.event.*; diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index 94bff0e..97f8147 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import java.awt.event.*; diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java index 2613df5..f652aae 100755 --- a/src/jalview/appletgui/PCAPanel.java +++ b/src/jalview/appletgui/PCAPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.datamodel.*; diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java index f696640..0f2c1f6 100755 --- a/src/jalview/appletgui/PaintRefresher.java +++ b/src/jalview/appletgui/PaintRefresher.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import java.awt.*; import java.util.*; diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java index 939e2f4..65f40c3 100755 --- a/src/jalview/appletgui/PairwiseAlignPanel.java +++ b/src/jalview/appletgui/PairwiseAlignPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.datamodel.*; diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java index 6e22ecb..735a579 100755 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.jbappletgui.*; diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java index ac42ad2..a13b1a2 100755 --- a/src/jalview/appletgui/RotatableCanvas.java +++ b/src/jalview/appletgui/RotatableCanvas.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.math.*; diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java index 51a03cc..24460ba 100755 --- a/src/jalview/appletgui/ScalePanel.java +++ b/src/jalview/appletgui/ScalePanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.datamodel.*; diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index e028819..6855468 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import java.awt.*; diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 3a707de..163b967 100755 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import java.awt.*; diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index dea4416..321edef 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.datamodel.*; diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java index 528f6c7..6c89fb7 100755 --- a/src/jalview/appletgui/SliderPanel.java +++ b/src/jalview/appletgui/SliderPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.jbappletgui.*; diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index f00fd17..be37813 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java index d6ee70e..c33975b 100755 --- a/src/jalview/appletgui/TreePanel.java +++ b/src/jalview/appletgui/TreePanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.datamodel.*; diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java index 071bad8..0c7e685 100755 --- a/src/jalview/appletgui/UserDefinedColours.java +++ b/src/jalview/appletgui/UserDefinedColours.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.appletgui; import jalview.jbappletgui.GUserDefinedColours; diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 226a925..d939a7e 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,11 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ - +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.bin; import java.util.*; diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 88e6236..2524abd 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,11 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ - +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.bin; diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 1ce2066..bd5abb0 100755 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.bin; import java.applet.*; diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java index 9a38f10..644cd03 100755 --- a/src/jalview/binding/Alignment.java +++ b/src/jalview/binding/Alignment.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,7 +42,7 @@ import org.xml.sax.ContentHandler; /** * Class Alignment. - * + * * @version $Revision$ $Date$ */ public class Alignment implements java.io.Serializable { @@ -59,31 +78,31 @@ public class Alignment implements java.io.Serializable { /** * Returns the value of field 'annotation'. - * + * * @return Annotation * @return the value of field 'annotation'. */ public jalview.binding.Annotation getAnnotation() { return this._annotation; - } //-- jalview.binding.Annotation getAnnotation() + } //-- jalview.binding.Annotation getAnnotation() /** * Returns the value of field 'sequenceSet'. - * + * * @return SequenceSet * @return the value of field 'sequenceSet'. */ public jalview.binding.SequenceSet getSequenceSet() { return this._sequenceSet; - } //-- jalview.binding.SequenceSet getSequenceSet() + } //-- jalview.binding.SequenceSet getSequenceSet() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -95,61 +114,61 @@ public class Alignment implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'annotation'. - * + * * @param annotation the value of field 'annotation'. */ public void setAnnotation(jalview.binding.Annotation annotation) { this._annotation = annotation; - } //-- void setAnnotation(jalview.binding.Annotation) + } //-- void setAnnotation(jalview.binding.Annotation) /** * Sets the value of field 'sequenceSet'. - * + * * @param sequenceSet the value of field 'sequenceSet'. */ public void setSequenceSet(jalview.binding.SequenceSet sequenceSet) { this._sequenceSet = sequenceSet; - } //-- void setSequenceSet(jalview.binding.SequenceSet) + } //-- void setSequenceSet(jalview.binding.SequenceSet) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -157,17 +176,17 @@ public class Alignment implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java index fefdd12..4af694f 100755 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -25,7 +44,7 @@ import org.xml.sax.ContentHandler; /** * Class Annotation. - * + * * @version $Revision$ $Date$ */ public class Annotation implements java.io.Serializable { @@ -77,22 +96,22 @@ public class Annotation implements java.io.Serializable { /** * Method addAnnotationElement - * - * - * + * + * + * * @param vAnnotationElement */ public void addAnnotationElement(jalview.binding.AnnotationElement vAnnotationElement) throws java.lang.IndexOutOfBoundsException { _annotationElementList.addElement(vAnnotationElement); - } //-- void addAnnotationElement(jalview.binding.AnnotationElement) + } //-- void addAnnotationElement(jalview.binding.AnnotationElement) /** * Method addAnnotationElement - * - * - * + * + * + * * @param index * @param vAnnotationElement */ @@ -100,34 +119,34 @@ public class Annotation implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _annotationElementList.insertElementAt(vAnnotationElement, index); - } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement) + } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement) /** * Method deleteGraph - * + * */ public void deleteGraph() { this._has_graph= false; - } //-- void deleteGraph() + } //-- void deleteGraph() /** * Method enumerateAnnotationElement - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateAnnotationElement() { return _annotationElementList.elements(); - } //-- java.util.Enumeration enumerateAnnotationElement() + } //-- java.util.Enumeration enumerateAnnotationElement() /** * Method getAnnotationElement - * - * - * + * + * + * * @param index * @return AnnotationElement */ @@ -138,15 +157,15 @@ public class Annotation implements java.io.Serializable { if ((index < 0) || (index > _annotationElementList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index); - } //-- jalview.binding.AnnotationElement getAnnotationElement(int) + } //-- jalview.binding.AnnotationElement getAnnotationElement(int) /** * Method getAnnotationElement - * - * - * + * + * + * * @return AnnotationElement */ public jalview.binding.AnnotationElement[] getAnnotationElement() @@ -157,70 +176,70 @@ public class Annotation implements java.io.Serializable { mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index); } return mArray; - } //-- jalview.binding.AnnotationElement[] getAnnotationElement() + } //-- jalview.binding.AnnotationElement[] getAnnotationElement() /** * Method getAnnotationElementCount - * - * - * + * + * + * * @return int */ public int getAnnotationElementCount() { return _annotationElementList.size(); - } //-- int getAnnotationElementCount() + } //-- int getAnnotationElementCount() /** * Returns the value of field 'description'. - * + * * @return String * @return the value of field 'description'. */ public java.lang.String getDescription() { return this._description; - } //-- java.lang.String getDescription() + } //-- java.lang.String getDescription() /** * Returns the value of field 'graph'. - * + * * @return boolean * @return the value of field 'graph'. */ public boolean getGraph() { return this._graph; - } //-- boolean getGraph() + } //-- boolean getGraph() /** * Returns the value of field 'label'. - * + * * @return String * @return the value of field 'label'. */ public java.lang.String getLabel() { return this._label; - } //-- java.lang.String getLabel() + } //-- java.lang.String getLabel() /** * Method hasGraph - * - * - * + * + * + * * @return boolean */ public boolean hasGraph() { return this._has_graph; - } //-- boolean hasGraph() + } //-- boolean hasGraph() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -232,50 +251,50 @@ public class Annotation implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllAnnotationElement - * + * */ public void removeAllAnnotationElement() { _annotationElementList.removeAllElements(); - } //-- void removeAllAnnotationElement() + } //-- void removeAllAnnotationElement() /** * Method removeAnnotationElement - * - * - * + * + * + * * @param index * @return AnnotationElement */ @@ -284,13 +303,13 @@ public class Annotation implements java.io.Serializable { java.lang.Object obj = _annotationElementList.elementAt(index); _annotationElementList.removeElementAt(index); return (jalview.binding.AnnotationElement) obj; - } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) + } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) /** * Method setAnnotationElement - * - * - * + * + * + * * @param index * @param vAnnotationElement */ @@ -302,13 +321,13 @@ public class Annotation implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _annotationElementList.setElementAt(vAnnotationElement, index); - } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) + } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) /** * Method setAnnotationElement - * - * - * + * + * + * * @param annotationElementArray */ public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray) @@ -318,44 +337,44 @@ public class Annotation implements java.io.Serializable { for (int i = 0; i < annotationElementArray.length; i++) { _annotationElementList.addElement(annotationElementArray[i]); } - } //-- void setAnnotationElement(jalview.binding.AnnotationElement) + } //-- void setAnnotationElement(jalview.binding.AnnotationElement) /** * Sets the value of field 'description'. - * + * * @param description the value of field 'description'. */ public void setDescription(java.lang.String description) { this._description = description; - } //-- void setDescription(java.lang.String) + } //-- void setDescription(java.lang.String) /** * Sets the value of field 'graph'. - * + * * @param graph the value of field 'graph'. */ public void setGraph(boolean graph) { this._graph = graph; this._has_graph = true; - } //-- void setGraph(boolean) + } //-- void setGraph(boolean) /** * Sets the value of field 'label'. - * + * * @param label the value of field 'label'. */ public void setLabel(java.lang.String label) { this._label = label; - } //-- void setLabel(java.lang.String) + } //-- void setLabel(java.lang.String) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -363,17 +382,17 @@ public class Annotation implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java index e4aec31..211810d 100755 --- a/src/jalview/binding/AnnotationElement.java +++ b/src/jalview/binding/AnnotationElement.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,7 +42,7 @@ import org.xml.sax.ContentHandler; /** * Class AnnotationElement. - * + * * @version $Revision$ $Date$ */ public class AnnotationElement implements java.io.Serializable { @@ -84,106 +103,106 @@ public class AnnotationElement implements java.io.Serializable { /** * Method deletePosition - * + * */ public void deletePosition() { this._has_position= false; - } //-- void deletePosition() + } //-- void deletePosition() /** * Method deleteValue - * + * */ public void deleteValue() { this._has_value= false; - } //-- void deleteValue() + } //-- void deleteValue() /** * Returns the value of field 'description'. - * + * * @return String * @return the value of field 'description'. */ public java.lang.String getDescription() { return this._description; - } //-- java.lang.String getDescription() + } //-- java.lang.String getDescription() /** * Returns the value of field 'displayCharacter'. - * + * * @return String * @return the value of field 'displayCharacter'. */ public java.lang.String getDisplayCharacter() { return this._displayCharacter; - } //-- java.lang.String getDisplayCharacter() + } //-- java.lang.String getDisplayCharacter() /** * Returns the value of field 'position'. - * + * * @return int * @return the value of field 'position'. */ public int getPosition() { return this._position; - } //-- int getPosition() + } //-- int getPosition() /** * Returns the value of field 'secondaryStructure'. - * + * * @return String * @return the value of field 'secondaryStructure'. */ public java.lang.String getSecondaryStructure() { return this._secondaryStructure; - } //-- java.lang.String getSecondaryStructure() + } //-- java.lang.String getSecondaryStructure() /** * Returns the value of field 'value'. - * + * * @return float * @return the value of field 'value'. */ public float getValue() { return this._value; - } //-- float getValue() + } //-- float getValue() /** * Method hasPosition - * - * - * + * + * + * * @return boolean */ public boolean hasPosition() { return this._has_position; - } //-- boolean hasPosition() + } //-- boolean hasPosition() /** * Method hasValue - * - * - * + * + * + * * @return boolean */ public boolean hasValue() { return this._has_value; - } //-- boolean hasValue() + } //-- boolean hasValue() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -195,94 +214,94 @@ public class AnnotationElement implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'description'. - * + * * @param description the value of field 'description'. */ public void setDescription(java.lang.String description) { this._description = description; - } //-- void setDescription(java.lang.String) + } //-- void setDescription(java.lang.String) /** * Sets the value of field 'displayCharacter'. - * + * * @param displayCharacter the value of field 'displayCharacter' */ public void setDisplayCharacter(java.lang.String displayCharacter) { this._displayCharacter = displayCharacter; - } //-- void setDisplayCharacter(java.lang.String) + } //-- void setDisplayCharacter(java.lang.String) /** * Sets the value of field 'position'. - * + * * @param position the value of field 'position'. */ public void setPosition(int position) { this._position = position; this._has_position = true; - } //-- void setPosition(int) + } //-- void setPosition(int) /** * Sets the value of field 'secondaryStructure'. - * + * * @param secondaryStructure the value of field * 'secondaryStructure'. */ public void setSecondaryStructure(java.lang.String secondaryStructure) { this._secondaryStructure = secondaryStructure; - } //-- void setSecondaryStructure(java.lang.String) + } //-- void setSecondaryStructure(java.lang.String) /** * Sets the value of field 'value'. - * + * * @param value the value of field 'value'. */ public void setValue(float value) { this._value = value; this._has_value = true; - } //-- void setValue(float) + } //-- void setValue(float) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -290,17 +309,17 @@ public class AnnotationElement implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java index a51102b..2a3423d 100755 --- a/src/jalview/binding/Colour.java +++ b/src/jalview/binding/Colour.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,7 +42,7 @@ import org.xml.sax.ContentHandler; /** * Class Colour. - * + * * @version $Revision$ $Date$ */ public class Colour implements java.io.Serializable { @@ -59,31 +78,31 @@ public class Colour implements java.io.Serializable { /** * Returns the value of field 'name'. - * + * * @return String * @return the value of field 'name'. */ public java.lang.String getName() { return this._name; - } //-- java.lang.String getName() + } //-- java.lang.String getName() /** * Returns the value of field 'RGB'. - * + * * @return String * @return the value of field 'RGB'. */ public java.lang.String getRGB() { return this._RGB; - } //-- java.lang.String getRGB() + } //-- java.lang.String getRGB() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -95,61 +114,61 @@ public class Colour implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'name'. - * + * * @param name the value of field 'name'. */ public void setName(java.lang.String name) { this._name = name; - } //-- void setName(java.lang.String) + } //-- void setName(java.lang.String) /** * Sets the value of field 'RGB'. - * + * * @param RGB the value of field 'RGB'. */ public void setRGB(java.lang.String RGB) { this._RGB = RGB; - } //-- void setRGB(java.lang.String) + } //-- void setRGB(java.lang.String) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -157,17 +176,17 @@ public class Colour implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java index 6473149..eef4a28 100755 --- a/src/jalview/binding/JGroup.java +++ b/src/jalview/binding/JGroup.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -25,7 +44,7 @@ import org.xml.sax.ContentHandler; /** * Class JGroup. - * + * * @version $Revision$ $Date$ */ public class JGroup implements java.io.Serializable { @@ -147,22 +166,22 @@ public class JGroup implements java.io.Serializable { /** * Method addSeq - * - * - * + * + * + * * @param vSeq */ public void addSeq(int vSeq) throws java.lang.IndexOutOfBoundsException { _seqList.addElement(new java.lang.Integer(vSeq)); - } //-- void addSeq(int) + } //-- void addSeq(int) /** * Method addSeq - * - * - * + * + * + * * @param index * @param vSeq */ @@ -170,196 +189,196 @@ public class JGroup implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _seqList.insertElementAt(new java.lang.Integer(vSeq), index); - } //-- void addSeq(int, int) + } //-- void addSeq(int, int) /** * Method deleteColourText - * + * */ public void deleteColourText() { this._has_colourText= false; - } //-- void deleteColourText() + } //-- void deleteColourText() /** * Method deleteConsThreshold - * + * */ public void deleteConsThreshold() { this._has_consThreshold= false; - } //-- void deleteConsThreshold() + } //-- void deleteConsThreshold() /** * Method deleteDisplayBoxes - * + * */ public void deleteDisplayBoxes() { this._has_displayBoxes= false; - } //-- void deleteDisplayBoxes() + } //-- void deleteDisplayBoxes() /** * Method deleteDisplayText - * + * */ public void deleteDisplayText() { this._has_displayText= false; - } //-- void deleteDisplayText() + } //-- void deleteDisplayText() /** * Method deleteEnd - * + * */ public void deleteEnd() { this._has_end= false; - } //-- void deleteEnd() + } //-- void deleteEnd() /** * Method deleteOutlineColour - * + * */ public void deleteOutlineColour() { this._has_outlineColour= false; - } //-- void deleteOutlineColour() + } //-- void deleteOutlineColour() /** * Method deletePidThreshold - * + * */ public void deletePidThreshold() { this._has_pidThreshold= false; - } //-- void deletePidThreshold() + } //-- void deletePidThreshold() /** * Method deleteStart - * + * */ public void deleteStart() { this._has_start= false; - } //-- void deleteStart() + } //-- void deleteStart() /** * Method enumerateSeq - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateSeq() { return _seqList.elements(); - } //-- java.util.Enumeration enumerateSeq() + } //-- java.util.Enumeration enumerateSeq() /** * Returns the value of field 'colour'. - * + * * @return String * @return the value of field 'colour'. */ public java.lang.String getColour() { return this._colour; - } //-- java.lang.String getColour() + } //-- java.lang.String getColour() /** * Returns the value of field 'colourText'. - * + * * @return boolean * @return the value of field 'colourText'. */ public boolean getColourText() { return this._colourText; - } //-- boolean getColourText() + } //-- boolean getColourText() /** * Returns the value of field 'consThreshold'. - * + * * @return int * @return the value of field 'consThreshold'. */ public int getConsThreshold() { return this._consThreshold; - } //-- int getConsThreshold() + } //-- int getConsThreshold() /** * Returns the value of field 'displayBoxes'. - * + * * @return boolean * @return the value of field 'displayBoxes'. */ public boolean getDisplayBoxes() { return this._displayBoxes; - } //-- boolean getDisplayBoxes() + } //-- boolean getDisplayBoxes() /** * Returns the value of field 'displayText'. - * + * * @return boolean * @return the value of field 'displayText'. */ public boolean getDisplayText() { return this._displayText; - } //-- boolean getDisplayText() + } //-- boolean getDisplayText() /** * Returns the value of field 'end'. - * + * * @return int * @return the value of field 'end'. */ public int getEnd() { return this._end; - } //-- int getEnd() + } //-- int getEnd() /** * Returns the value of field 'name'. - * + * * @return String * @return the value of field 'name'. */ public java.lang.String getName() { return this._name; - } //-- java.lang.String getName() + } //-- java.lang.String getName() /** * Returns the value of field 'outlineColour'. - * + * * @return int * @return the value of field 'outlineColour'. */ public int getOutlineColour() { return this._outlineColour; - } //-- int getOutlineColour() + } //-- int getOutlineColour() /** * Returns the value of field 'pidThreshold'. - * + * * @return int * @return the value of field 'pidThreshold'. */ public int getPidThreshold() { return this._pidThreshold; - } //-- int getPidThreshold() + } //-- int getPidThreshold() /** * Method getSeq - * - * - * + * + * + * * @param index * @return int */ @@ -370,15 +389,15 @@ public class JGroup implements java.io.Serializable { if ((index < 0) || (index > _seqList.size())) { throw new IndexOutOfBoundsException(); } - + return ((java.lang.Integer)_seqList.elementAt(index)).intValue(); - } //-- int getSeq(int) + } //-- int getSeq(int) /** * Method getSeq - * - * - * + * + * + * * @return int */ public int[] getSeq() @@ -389,132 +408,132 @@ public class JGroup implements java.io.Serializable { mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue(); } return mArray; - } //-- int[] getSeq() + } //-- int[] getSeq() /** * Method getSeqCount - * - * - * + * + * + * * @return int */ public int getSeqCount() { return _seqList.size(); - } //-- int getSeqCount() + } //-- int getSeqCount() /** * Returns the value of field 'start'. - * + * * @return int * @return the value of field 'start'. */ public int getStart() { return this._start; - } //-- int getStart() + } //-- int getStart() /** * Method hasColourText - * - * - * + * + * + * * @return boolean */ public boolean hasColourText() { return this._has_colourText; - } //-- boolean hasColourText() + } //-- boolean hasColourText() /** * Method hasConsThreshold - * - * - * + * + * + * * @return boolean */ public boolean hasConsThreshold() { return this._has_consThreshold; - } //-- boolean hasConsThreshold() + } //-- boolean hasConsThreshold() /** * Method hasDisplayBoxes - * - * - * + * + * + * * @return boolean */ public boolean hasDisplayBoxes() { return this._has_displayBoxes; - } //-- boolean hasDisplayBoxes() + } //-- boolean hasDisplayBoxes() /** * Method hasDisplayText - * - * - * + * + * + * * @return boolean */ public boolean hasDisplayText() { return this._has_displayText; - } //-- boolean hasDisplayText() + } //-- boolean hasDisplayText() /** * Method hasEnd - * - * - * + * + * + * * @return boolean */ public boolean hasEnd() { return this._has_end; - } //-- boolean hasEnd() + } //-- boolean hasEnd() /** * Method hasOutlineColour - * - * - * + * + * + * * @return boolean */ public boolean hasOutlineColour() { return this._has_outlineColour; - } //-- boolean hasOutlineColour() + } //-- boolean hasOutlineColour() /** * Method hasPidThreshold - * - * - * + * + * + * * @return boolean */ public boolean hasPidThreshold() { return this._has_pidThreshold; - } //-- boolean hasPidThreshold() + } //-- boolean hasPidThreshold() /** * Method hasStart - * - * - * + * + * + * * @return boolean */ public boolean hasStart() { return this._has_start; - } //-- boolean hasStart() + } //-- boolean hasStart() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -526,50 +545,50 @@ public class JGroup implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllSeq - * + * */ public void removeAllSeq() { _seqList.removeAllElements(); - } //-- void removeAllSeq() + } //-- void removeAllSeq() /** * Method removeSeq - * - * - * + * + * + * * @param index * @return int */ @@ -578,110 +597,110 @@ public class JGroup implements java.io.Serializable { java.lang.Object obj = _seqList.elementAt(index); _seqList.removeElementAt(index); return ((java.lang.Integer)obj).intValue(); - } //-- int removeSeq(int) + } //-- int removeSeq(int) /** * Sets the value of field 'colour'. - * + * * @param colour the value of field 'colour'. */ public void setColour(java.lang.String colour) { this._colour = colour; - } //-- void setColour(java.lang.String) + } //-- void setColour(java.lang.String) /** * Sets the value of field 'colourText'. - * + * * @param colourText the value of field 'colourText'. */ public void setColourText(boolean colourText) { this._colourText = colourText; this._has_colourText = true; - } //-- void setColourText(boolean) + } //-- void setColourText(boolean) /** * Sets the value of field 'consThreshold'. - * + * * @param consThreshold the value of field 'consThreshold'. */ public void setConsThreshold(int consThreshold) { this._consThreshold = consThreshold; this._has_consThreshold = true; - } //-- void setConsThreshold(int) + } //-- void setConsThreshold(int) /** * Sets the value of field 'displayBoxes'. - * + * * @param displayBoxes the value of field 'displayBoxes'. */ public void setDisplayBoxes(boolean displayBoxes) { this._displayBoxes = displayBoxes; this._has_displayBoxes = true; - } //-- void setDisplayBoxes(boolean) + } //-- void setDisplayBoxes(boolean) /** * Sets the value of field 'displayText'. - * + * * @param displayText the value of field 'displayText'. */ public void setDisplayText(boolean displayText) { this._displayText = displayText; this._has_displayText = true; - } //-- void setDisplayText(boolean) + } //-- void setDisplayText(boolean) /** * Sets the value of field 'end'. - * + * * @param end the value of field 'end'. */ public void setEnd(int end) { this._end = end; this._has_end = true; - } //-- void setEnd(int) + } //-- void setEnd(int) /** * Sets the value of field 'name'. - * + * * @param name the value of field 'name'. */ public void setName(java.lang.String name) { this._name = name; - } //-- void setName(java.lang.String) + } //-- void setName(java.lang.String) /** * Sets the value of field 'outlineColour'. - * + * * @param outlineColour the value of field 'outlineColour'. */ public void setOutlineColour(int outlineColour) { this._outlineColour = outlineColour; this._has_outlineColour = true; - } //-- void setOutlineColour(int) + } //-- void setOutlineColour(int) /** * Sets the value of field 'pidThreshold'. - * + * * @param pidThreshold the value of field 'pidThreshold'. */ public void setPidThreshold(int pidThreshold) { this._pidThreshold = pidThreshold; this._has_pidThreshold = true; - } //-- void setPidThreshold(int) + } //-- void setPidThreshold(int) /** * Method setSeq - * - * - * + * + * + * * @param index * @param vSeq */ @@ -693,13 +712,13 @@ public class JGroup implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _seqList.setElementAt(new java.lang.Integer(vSeq), index); - } //-- void setSeq(int, int) + } //-- void setSeq(int, int) /** * Method setSeq - * - * - * + * + * + * * @param seqArray */ public void setSeq(int[] seqArray) @@ -709,24 +728,24 @@ public class JGroup implements java.io.Serializable { for (int i = 0; i < seqArray.length; i++) { _seqList.addElement(new java.lang.Integer(seqArray[i])); } - } //-- void setSeq(int) + } //-- void setSeq(int) /** * Sets the value of field 'start'. - * + * * @param start the value of field 'start'. */ public void setStart(int start) { this._start = start; this._has_start = true; - } //-- void setStart(int) + } //-- void setStart(int) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -734,17 +753,17 @@ public class JGroup implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java index 751409f..9e02e60 100755 --- a/src/jalview/binding/JSeq.java +++ b/src/jalview/binding/JSeq.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,7 +42,7 @@ import org.xml.sax.ContentHandler; /** * Class JSeq. - * + * * @version $Revision$ $Date$ */ public class JSeq implements java.io.Serializable { @@ -89,137 +108,137 @@ public class JSeq implements java.io.Serializable { /** * Method deleteColour - * + * */ public void deleteColour() { this._has_colour= false; - } //-- void deleteColour() + } //-- void deleteColour() /** * Method deleteEnd - * + * */ public void deleteEnd() { this._has_end= false; - } //-- void deleteEnd() + } //-- void deleteEnd() /** * Method deleteId - * + * */ public void deleteId() { this._has_id= false; - } //-- void deleteId() + } //-- void deleteId() /** * Method deleteStart - * + * */ public void deleteStart() { this._has_start= false; - } //-- void deleteStart() + } //-- void deleteStart() /** * Returns the value of field 'colour'. - * + * * @return int * @return the value of field 'colour'. */ public int getColour() { return this._colour; - } //-- int getColour() + } //-- int getColour() /** * Returns the value of field 'end'. - * + * * @return int * @return the value of field 'end'. */ public int getEnd() { return this._end; - } //-- int getEnd() + } //-- int getEnd() /** * Returns the value of field 'id'. - * + * * @return int * @return the value of field 'id'. */ public int getId() { return this._id; - } //-- int getId() + } //-- int getId() /** * Returns the value of field 'start'. - * + * * @return int * @return the value of field 'start'. */ public int getStart() { return this._start; - } //-- int getStart() + } //-- int getStart() /** * Method hasColour - * - * - * + * + * + * * @return boolean */ public boolean hasColour() { return this._has_colour; - } //-- boolean hasColour() + } //-- boolean hasColour() /** * Method hasEnd - * - * - * + * + * + * * @return boolean */ public boolean hasEnd() { return this._has_end; - } //-- boolean hasEnd() + } //-- boolean hasEnd() /** * Method hasId - * - * - * + * + * + * * @return boolean */ public boolean hasId() { return this._has_id; - } //-- boolean hasId() + } //-- boolean hasId() /** * Method hasStart - * - * - * + * + * + * * @return boolean */ public boolean hasStart() { return this._has_start; - } //-- boolean hasStart() + } //-- boolean hasStart() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -231,85 +250,85 @@ public class JSeq implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'colour'. - * + * * @param colour the value of field 'colour'. */ public void setColour(int colour) { this._colour = colour; this._has_colour = true; - } //-- void setColour(int) + } //-- void setColour(int) /** * Sets the value of field 'end'. - * + * * @param end the value of field 'end'. */ public void setEnd(int end) { this._end = end; this._has_end = true; - } //-- void setEnd(int) + } //-- void setEnd(int) /** * Sets the value of field 'id'. - * + * * @param id the value of field 'id'. */ public void setId(int id) { this._id = id; this._has_id = true; - } //-- void setId(int) + } //-- void setId(int) /** * Sets the value of field 'start'. - * + * * @param start the value of field 'start'. */ public void setStart(int start) { this._start = start; this._has_start = true; - } //-- void setStart(int) + } //-- void setStart(int) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -317,17 +336,17 @@ public class JSeq implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java index a558b10..d30e97d 100755 --- a/src/jalview/binding/JalviewModel.java +++ b/src/jalview/binding/JalviewModel.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -24,7 +43,7 @@ import org.xml.sax.ContentHandler; /** * Class JalviewModel. - * + * * @version $Revision$ $Date$ */ public class JalviewModel implements java.io.Serializable { @@ -65,42 +84,42 @@ public class JalviewModel implements java.io.Serializable { /** * Returns the value of field 'creationDate'. - * + * * @return Date * @return the value of field 'creationDate'. */ public java.util.Date getCreationDate() { return this._creationDate; - } //-- java.util.Date getCreationDate() + } //-- java.util.Date getCreationDate() /** * Returns the value of field 'jalviewModelSequence'. - * + * * @return JalviewModelSequence * @return the value of field 'jalviewModelSequence'. */ public jalview.binding.JalviewModelSequence getJalviewModelSequence() { return this._jalviewModelSequence; - } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() + } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() /** * Returns the value of field 'vamsasModel'. - * + * * @return VamsasModel * @return the value of field 'vamsasModel'. */ public jalview.binding.VamsasModel getVamsasModel() { return this._vamsasModel; - } //-- jalview.binding.VamsasModel getVamsasModel() + } //-- jalview.binding.VamsasModel getVamsasModel() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -112,72 +131,72 @@ public class JalviewModel implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'creationDate'. - * + * * @param creationDate the value of field 'creationDate'. */ public void setCreationDate(java.util.Date creationDate) { this._creationDate = creationDate; - } //-- void setCreationDate(java.util.Date) + } //-- void setCreationDate(java.util.Date) /** * Sets the value of field 'jalviewModelSequence'. - * + * * @param jalviewModelSequence the value of field * 'jalviewModelSequence'. */ public void setJalviewModelSequence(jalview.binding.JalviewModelSequence jalviewModelSequence) { this._jalviewModelSequence = jalviewModelSequence; - } //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) + } //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) /** * Sets the value of field 'vamsasModel'. - * + * * @param vamsasModel the value of field 'vamsasModel'. */ public void setVamsasModel(jalview.binding.VamsasModel vamsasModel) { this._vamsasModel = vamsasModel; - } //-- void setVamsasModel(jalview.binding.VamsasModel) + } //-- void setVamsasModel(jalview.binding.VamsasModel) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -185,17 +204,17 @@ public class JalviewModel implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java index 61c80aa..d22dcd4 100755 --- a/src/jalview/binding/JalviewModelSequence.java +++ b/src/jalview/binding/JalviewModelSequence.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -25,7 +44,7 @@ import org.xml.sax.ContentHandler; /** * Class JalviewModelSequence. - * + * * @version $Revision$ $Date$ */ public class JalviewModelSequence implements java.io.Serializable { @@ -75,22 +94,22 @@ public class JalviewModelSequence implements java.io.Serializable { /** * Method addJGroup - * - * - * + * + * + * * @param vJGroup */ public void addJGroup(jalview.binding.JGroup vJGroup) throws java.lang.IndexOutOfBoundsException { _JGroupList.addElement(vJGroup); - } //-- void addJGroup(jalview.binding.JGroup) + } //-- void addJGroup(jalview.binding.JGroup) /** * Method addJGroup - * - * - * + * + * + * * @param index * @param vJGroup */ @@ -98,26 +117,26 @@ public class JalviewModelSequence implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _JGroupList.insertElementAt(vJGroup, index); - } //-- void addJGroup(int, jalview.binding.JGroup) + } //-- void addJGroup(int, jalview.binding.JGroup) /** * Method addJSeq - * - * - * + * + * + * * @param vJSeq */ public void addJSeq(jalview.binding.JSeq vJSeq) throws java.lang.IndexOutOfBoundsException { _JSeqList.addElement(vJSeq); - } //-- void addJSeq(jalview.binding.JSeq) + } //-- void addJSeq(jalview.binding.JSeq) /** * Method addJSeq - * - * - * + * + * + * * @param index * @param vJSeq */ @@ -125,26 +144,26 @@ public class JalviewModelSequence implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _JSeqList.insertElementAt(vJSeq, index); - } //-- void addJSeq(int, jalview.binding.JSeq) + } //-- void addJSeq(int, jalview.binding.JSeq) /** * Method addUserColours - * - * - * + * + * + * * @param vUserColours */ public void addUserColours(jalview.binding.UserColours vUserColours) throws java.lang.IndexOutOfBoundsException { _userColoursList.addElement(vUserColours); - } //-- void addUserColours(jalview.binding.UserColours) + } //-- void addUserColours(jalview.binding.UserColours) /** * Method addUserColours - * - * - * + * + * + * * @param index * @param vUserColours */ @@ -152,26 +171,26 @@ public class JalviewModelSequence implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _userColoursList.insertElementAt(vUserColours, index); - } //-- void addUserColours(int, jalview.binding.UserColours) + } //-- void addUserColours(int, jalview.binding.UserColours) /** * Method addViewport - * - * - * + * + * + * * @param vViewport */ public void addViewport(jalview.binding.Viewport vViewport) throws java.lang.IndexOutOfBoundsException { _viewportList.addElement(vViewport); - } //-- void addViewport(jalview.binding.Viewport) + } //-- void addViewport(jalview.binding.Viewport) /** * Method addViewport - * - * - * + * + * + * * @param index * @param vViewport */ @@ -179,61 +198,61 @@ public class JalviewModelSequence implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _viewportList.insertElementAt(vViewport, index); - } //-- void addViewport(int, jalview.binding.Viewport) + } //-- void addViewport(int, jalview.binding.Viewport) /** * Method enumerateJGroup - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateJGroup() { return _JGroupList.elements(); - } //-- java.util.Enumeration enumerateJGroup() + } //-- java.util.Enumeration enumerateJGroup() /** * Method enumerateJSeq - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateJSeq() { return _JSeqList.elements(); - } //-- java.util.Enumeration enumerateJSeq() + } //-- java.util.Enumeration enumerateJSeq() /** * Method enumerateUserColours - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateUserColours() { return _userColoursList.elements(); - } //-- java.util.Enumeration enumerateUserColours() + } //-- java.util.Enumeration enumerateUserColours() /** * Method enumerateViewport - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateViewport() { return _viewportList.elements(); - } //-- java.util.Enumeration enumerateViewport() + } //-- java.util.Enumeration enumerateViewport() /** * Method getJGroup - * - * - * + * + * + * * @param index * @return JGroup */ @@ -244,15 +263,15 @@ public class JalviewModelSequence implements java.io.Serializable { if ((index < 0) || (index > _JGroupList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.JGroup) _JGroupList.elementAt(index); - } //-- jalview.binding.JGroup getJGroup(int) + } //-- jalview.binding.JGroup getJGroup(int) /** * Method getJGroup - * - * - * + * + * + * * @return JGroup */ public jalview.binding.JGroup[] getJGroup() @@ -263,25 +282,25 @@ public class JalviewModelSequence implements java.io.Serializable { mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index); } return mArray; - } //-- jalview.binding.JGroup[] getJGroup() + } //-- jalview.binding.JGroup[] getJGroup() /** * Method getJGroupCount - * - * - * + * + * + * * @return int */ public int getJGroupCount() { return _JGroupList.size(); - } //-- int getJGroupCount() + } //-- int getJGroupCount() /** * Method getJSeq - * - * - * + * + * + * * @param index * @return JSeq */ @@ -292,15 +311,15 @@ public class JalviewModelSequence implements java.io.Serializable { if ((index < 0) || (index > _JSeqList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.JSeq) _JSeqList.elementAt(index); - } //-- jalview.binding.JSeq getJSeq(int) + } //-- jalview.binding.JSeq getJSeq(int) /** * Method getJSeq - * - * - * + * + * + * * @return JSeq */ public jalview.binding.JSeq[] getJSeq() @@ -311,25 +330,25 @@ public class JalviewModelSequence implements java.io.Serializable { mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index); } return mArray; - } //-- jalview.binding.JSeq[] getJSeq() + } //-- jalview.binding.JSeq[] getJSeq() /** * Method getJSeqCount - * - * - * + * + * + * * @return int */ public int getJSeqCount() { return _JSeqList.size(); - } //-- int getJSeqCount() + } //-- int getJSeqCount() /** * Method getUserColours - * - * - * + * + * + * * @param index * @return UserColours */ @@ -340,15 +359,15 @@ public class JalviewModelSequence implements java.io.Serializable { if ((index < 0) || (index > _userColoursList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.UserColours) _userColoursList.elementAt(index); - } //-- jalview.binding.UserColours getUserColours(int) + } //-- jalview.binding.UserColours getUserColours(int) /** * Method getUserColours - * - * - * + * + * + * * @return UserColours */ public jalview.binding.UserColours[] getUserColours() @@ -359,25 +378,25 @@ public class JalviewModelSequence implements java.io.Serializable { mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index); } return mArray; - } //-- jalview.binding.UserColours[] getUserColours() + } //-- jalview.binding.UserColours[] getUserColours() /** * Method getUserColoursCount - * - * - * + * + * + * * @return int */ public int getUserColoursCount() { return _userColoursList.size(); - } //-- int getUserColoursCount() + } //-- int getUserColoursCount() /** * Method getViewport - * - * - * + * + * + * * @param index * @return Viewport */ @@ -388,15 +407,15 @@ public class JalviewModelSequence implements java.io.Serializable { if ((index < 0) || (index > _viewportList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.Viewport) _viewportList.elementAt(index); - } //-- jalview.binding.Viewport getViewport(int) + } //-- jalview.binding.Viewport getViewport(int) /** * Method getViewport - * - * - * + * + * + * * @return Viewport */ public jalview.binding.Viewport[] getViewport() @@ -407,25 +426,25 @@ public class JalviewModelSequence implements java.io.Serializable { mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index); } return mArray; - } //-- jalview.binding.Viewport[] getViewport() + } //-- jalview.binding.Viewport[] getViewport() /** * Method getViewportCount - * - * - * + * + * + * * @return int */ public int getViewportCount() { return _viewportList.size(); - } //-- int getViewportCount() + } //-- int getViewportCount() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -437,77 +456,77 @@ public class JalviewModelSequence implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllJGroup - * + * */ public void removeAllJGroup() { _JGroupList.removeAllElements(); - } //-- void removeAllJGroup() + } //-- void removeAllJGroup() /** * Method removeAllJSeq - * + * */ public void removeAllJSeq() { _JSeqList.removeAllElements(); - } //-- void removeAllJSeq() + } //-- void removeAllJSeq() /** * Method removeAllUserColours - * + * */ public void removeAllUserColours() { _userColoursList.removeAllElements(); - } //-- void removeAllUserColours() + } //-- void removeAllUserColours() /** * Method removeAllViewport - * + * */ public void removeAllViewport() { _viewportList.removeAllElements(); - } //-- void removeAllViewport() + } //-- void removeAllViewport() /** * Method removeJGroup - * - * - * + * + * + * * @param index * @return JGroup */ @@ -516,13 +535,13 @@ public class JalviewModelSequence implements java.io.Serializable { java.lang.Object obj = _JGroupList.elementAt(index); _JGroupList.removeElementAt(index); return (jalview.binding.JGroup) obj; - } //-- jalview.binding.JGroup removeJGroup(int) + } //-- jalview.binding.JGroup removeJGroup(int) /** * Method removeJSeq - * - * - * + * + * + * * @param index * @return JSeq */ @@ -531,13 +550,13 @@ public class JalviewModelSequence implements java.io.Serializable { java.lang.Object obj = _JSeqList.elementAt(index); _JSeqList.removeElementAt(index); return (jalview.binding.JSeq) obj; - } //-- jalview.binding.JSeq removeJSeq(int) + } //-- jalview.binding.JSeq removeJSeq(int) /** * Method removeUserColours - * - * - * + * + * + * * @param index * @return UserColours */ @@ -546,13 +565,13 @@ public class JalviewModelSequence implements java.io.Serializable { java.lang.Object obj = _userColoursList.elementAt(index); _userColoursList.removeElementAt(index); return (jalview.binding.UserColours) obj; - } //-- jalview.binding.UserColours removeUserColours(int) + } //-- jalview.binding.UserColours removeUserColours(int) /** * Method removeViewport - * - * - * + * + * + * * @param index * @return Viewport */ @@ -561,13 +580,13 @@ public class JalviewModelSequence implements java.io.Serializable { java.lang.Object obj = _viewportList.elementAt(index); _viewportList.removeElementAt(index); return (jalview.binding.Viewport) obj; - } //-- jalview.binding.Viewport removeViewport(int) + } //-- jalview.binding.Viewport removeViewport(int) /** * Method setJGroup - * - * - * + * + * + * * @param index * @param vJGroup */ @@ -579,13 +598,13 @@ public class JalviewModelSequence implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _JGroupList.setElementAt(vJGroup, index); - } //-- void setJGroup(int, jalview.binding.JGroup) + } //-- void setJGroup(int, jalview.binding.JGroup) /** * Method setJGroup - * - * - * + * + * + * * @param JGroupArray */ public void setJGroup(jalview.binding.JGroup[] JGroupArray) @@ -595,13 +614,13 @@ public class JalviewModelSequence implements java.io.Serializable { for (int i = 0; i < JGroupArray.length; i++) { _JGroupList.addElement(JGroupArray[i]); } - } //-- void setJGroup(jalview.binding.JGroup) + } //-- void setJGroup(jalview.binding.JGroup) /** * Method setJSeq - * - * - * + * + * + * * @param index * @param vJSeq */ @@ -613,13 +632,13 @@ public class JalviewModelSequence implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _JSeqList.setElementAt(vJSeq, index); - } //-- void setJSeq(int, jalview.binding.JSeq) + } //-- void setJSeq(int, jalview.binding.JSeq) /** * Method setJSeq - * - * - * + * + * + * * @param JSeqArray */ public void setJSeq(jalview.binding.JSeq[] JSeqArray) @@ -629,13 +648,13 @@ public class JalviewModelSequence implements java.io.Serializable { for (int i = 0; i < JSeqArray.length; i++) { _JSeqList.addElement(JSeqArray[i]); } - } //-- void setJSeq(jalview.binding.JSeq) + } //-- void setJSeq(jalview.binding.JSeq) /** * Method setUserColours - * - * - * + * + * + * * @param index * @param vUserColours */ @@ -647,13 +666,13 @@ public class JalviewModelSequence implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _userColoursList.setElementAt(vUserColours, index); - } //-- void setUserColours(int, jalview.binding.UserColours) + } //-- void setUserColours(int, jalview.binding.UserColours) /** * Method setUserColours - * - * - * + * + * + * * @param userColoursArray */ public void setUserColours(jalview.binding.UserColours[] userColoursArray) @@ -663,13 +682,13 @@ public class JalviewModelSequence implements java.io.Serializable { for (int i = 0; i < userColoursArray.length; i++) { _userColoursList.addElement(userColoursArray[i]); } - } //-- void setUserColours(jalview.binding.UserColours) + } //-- void setUserColours(jalview.binding.UserColours) /** * Method setViewport - * - * - * + * + * + * * @param index * @param vViewport */ @@ -681,13 +700,13 @@ public class JalviewModelSequence implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _viewportList.setElementAt(vViewport, index); - } //-- void setViewport(int, jalview.binding.Viewport) + } //-- void setViewport(int, jalview.binding.Viewport) /** * Method setViewport - * - * - * + * + * + * * @param viewportArray */ public void setViewport(jalview.binding.Viewport[] viewportArray) @@ -697,13 +716,13 @@ public class JalviewModelSequence implements java.io.Serializable { for (int i = 0; i < viewportArray.length; i++) { _viewportList.addElement(viewportArray[i]); } - } //-- void setViewport(jalview.binding.Viewport) + } //-- void setViewport(jalview.binding.Viewport) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -711,17 +730,17 @@ public class JalviewModelSequence implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/JalviewModelSequence2.java b/src/jalview/binding/JalviewModelSequence2.java index 36e5579..0cf1942 100755 --- a/src/jalview/binding/JalviewModelSequence2.java +++ b/src/jalview/binding/JalviewModelSequence2.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -25,7 +44,7 @@ import org.xml.sax.ContentHandler; /** * Class JalviewModelSequence2. - * + * * @version $Revision$ $Date$ */ public class JalviewModelSequence2 implements java.io.Serializable { @@ -57,22 +76,22 @@ public class JalviewModelSequence2 implements java.io.Serializable { /** * Method addJalviewModelSequence2Item - * - * - * + * + * + * * @param vJalviewModelSequence2Item */ public void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item) throws java.lang.IndexOutOfBoundsException { _items.addElement(vJalviewModelSequence2Item); - } //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) + } //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) /** * Method addJalviewModelSequence2Item - * - * - * + * + * + * * @param index * @param vJalviewModelSequence2Item */ @@ -80,25 +99,25 @@ public class JalviewModelSequence2 implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _items.insertElementAt(vJalviewModelSequence2Item, index); - } //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) + } //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) /** * Method enumerateJalviewModelSequence2Item - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateJalviewModelSequence2Item() { return _items.elements(); - } //-- java.util.Enumeration enumerateJalviewModelSequence2Item() + } //-- java.util.Enumeration enumerateJalviewModelSequence2Item() /** * Method getJalviewModelSequence2Item - * - * - * + * + * + * * @param index * @return JalviewModelSequence2Item */ @@ -109,15 +128,15 @@ public class JalviewModelSequence2 implements java.io.Serializable { if ((index < 0) || (index > _items.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index); - } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) + } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) /** * Method getJalviewModelSequence2Item - * - * - * + * + * + * * @return JalviewModelSequence2Item */ public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() @@ -128,25 +147,25 @@ public class JalviewModelSequence2 implements java.io.Serializable { mArray[index] = (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index); } return mArray; - } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() + } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() /** * Method getJalviewModelSequence2ItemCount - * - * - * + * + * + * * @return int */ public int getJalviewModelSequence2ItemCount() { return _items.size(); - } //-- int getJalviewModelSequence2ItemCount() + } //-- int getJalviewModelSequence2ItemCount() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -158,50 +177,50 @@ public class JalviewModelSequence2 implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllJalviewModelSequence2Item - * + * */ public void removeAllJalviewModelSequence2Item() { _items.removeAllElements(); - } //-- void removeAllJalviewModelSequence2Item() + } //-- void removeAllJalviewModelSequence2Item() /** * Method removeJalviewModelSequence2Item - * - * - * + * + * + * * @param index * @return JalviewModelSequence2Item */ @@ -210,13 +229,13 @@ public class JalviewModelSequence2 implements java.io.Serializable { java.lang.Object obj = _items.elementAt(index); _items.removeElementAt(index); return (jalview.binding.JalviewModelSequence2Item) obj; - } //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) + } //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) /** * Method setJalviewModelSequence2Item - * - * - * + * + * + * * @param index * @param vJalviewModelSequence2Item */ @@ -228,13 +247,13 @@ public class JalviewModelSequence2 implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _items.setElementAt(vJalviewModelSequence2Item, index); - } //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) + } //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) /** * Method setJalviewModelSequence2Item - * - * - * + * + * + * * @param jalviewModelSequence2ItemArray */ public void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray) @@ -244,13 +263,13 @@ public class JalviewModelSequence2 implements java.io.Serializable { for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++) { _items.addElement(jalviewModelSequence2ItemArray[i]); } - } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) + } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -258,17 +277,17 @@ public class JalviewModelSequence2 implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/JalviewModelSequence2Item.java b/src/jalview/binding/JalviewModelSequence2Item.java index 8678b09..dcd3ebc 100755 --- a/src/jalview/binding/JalviewModelSequence2Item.java +++ b/src/jalview/binding/JalviewModelSequence2Item.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -19,7 +38,7 @@ import org.exolab.castor.xml.Unmarshaller; /** * Class JalviewModelSequence2Item. - * + * * @version $Revision$ $Date$ */ public class JalviewModelSequence2Item implements java.io.Serializable { @@ -51,22 +70,22 @@ public class JalviewModelSequence2Item implements java.io.Serializable { /** * Method addUserColourScheme - * - * - * + * + * + * * @param vUserColourScheme */ public void addUserColourScheme(jalview.binding.UserColourScheme vUserColourScheme) throws java.lang.IndexOutOfBoundsException { _userColourSchemeList.addElement(vUserColourScheme); - } //-- void addUserColourScheme(jalview.binding.UserColourScheme) + } //-- void addUserColourScheme(jalview.binding.UserColourScheme) /** * Method addUserColourScheme - * - * - * + * + * + * * @param index * @param vUserColourScheme */ @@ -74,25 +93,25 @@ public class JalviewModelSequence2Item implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _userColourSchemeList.insertElementAt(vUserColourScheme, index); - } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme) + } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme) /** * Method enumerateUserColourScheme - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateUserColourScheme() { return _userColourSchemeList.elements(); - } //-- java.util.Enumeration enumerateUserColourScheme() + } //-- java.util.Enumeration enumerateUserColourScheme() /** * Method getUserColourScheme - * - * - * + * + * + * * @param index * @return UserColourScheme */ @@ -103,15 +122,15 @@ public class JalviewModelSequence2Item implements java.io.Serializable { if ((index < 0) || (index > _userColourSchemeList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index); - } //-- jalview.binding.UserColourScheme getUserColourScheme(int) + } //-- jalview.binding.UserColourScheme getUserColourScheme(int) /** * Method getUserColourScheme - * - * - * + * + * + * * @return UserColourScheme */ public jalview.binding.UserColourScheme[] getUserColourScheme() @@ -122,34 +141,34 @@ public class JalviewModelSequence2Item implements java.io.Serializable { mArray[index] = (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index); } return mArray; - } //-- jalview.binding.UserColourScheme[] getUserColourScheme() + } //-- jalview.binding.UserColourScheme[] getUserColourScheme() /** * Method getUserColourSchemeCount - * - * - * + * + * + * * @return int */ public int getUserColourSchemeCount() { return _userColourSchemeList.size(); - } //-- int getUserColourSchemeCount() + } //-- int getUserColourSchemeCount() /** * Method removeAllUserColourScheme - * + * */ public void removeAllUserColourScheme() { _userColourSchemeList.removeAllElements(); - } //-- void removeAllUserColourScheme() + } //-- void removeAllUserColourScheme() /** * Method removeUserColourScheme - * - * - * + * + * + * * @param index * @return UserColourScheme */ @@ -158,13 +177,13 @@ public class JalviewModelSequence2Item implements java.io.Serializable { java.lang.Object obj = _userColourSchemeList.elementAt(index); _userColourSchemeList.removeElementAt(index); return (jalview.binding.UserColourScheme) obj; - } //-- jalview.binding.UserColourScheme removeUserColourScheme(int) + } //-- jalview.binding.UserColourScheme removeUserColourScheme(int) /** * Method setUserColourScheme - * - * - * + * + * + * * @param index * @param vUserColourScheme */ @@ -176,13 +195,13 @@ public class JalviewModelSequence2Item implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _userColourSchemeList.setElementAt(vUserColourScheme, index); - } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme) + } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme) /** * Method setUserColourScheme - * - * - * + * + * + * * @param userColourSchemeArray */ public void setUserColourScheme(jalview.binding.UserColourScheme[] userColourSchemeArray) @@ -192,6 +211,6 @@ public class JalviewModelSequence2Item implements java.io.Serializable { for (int i = 0; i < userColourSchemeArray.length; i++) { _userColourSchemeList.addElement(userColourSchemeArray[i]); } - } //-- void setUserColourScheme(jalview.binding.UserColourScheme) + } //-- void setUserColourScheme(jalview.binding.UserColourScheme) } diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java index 676a623..354dc2f 100755 --- a/src/jalview/binding/JalviewUserColours.java +++ b/src/jalview/binding/JalviewUserColours.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -25,7 +44,7 @@ import org.xml.sax.ContentHandler; /** * Class JalviewUserColours. - * + * * @version $Revision$ $Date$ */ public class JalviewUserColours implements java.io.Serializable { @@ -57,22 +76,22 @@ public class JalviewUserColours implements java.io.Serializable { /** * Method addColour - * - * - * + * + * + * * @param vColour */ public void addColour(jalview.binding.Colour vColour) throws java.lang.IndexOutOfBoundsException { _colourList.addElement(vColour); - } //-- void addColour(jalview.binding.Colour) + } //-- void addColour(jalview.binding.Colour) /** * Method addColour - * - * - * + * + * + * * @param index * @param vColour */ @@ -80,25 +99,25 @@ public class JalviewUserColours implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _colourList.insertElementAt(vColour, index); - } //-- void addColour(int, jalview.binding.Colour) + } //-- void addColour(int, jalview.binding.Colour) /** * Method enumerateColour - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateColour() { return _colourList.elements(); - } //-- java.util.Enumeration enumerateColour() + } //-- java.util.Enumeration enumerateColour() /** * Method getColour - * - * - * + * + * + * * @param index * @return Colour */ @@ -109,15 +128,15 @@ public class JalviewUserColours implements java.io.Serializable { if ((index < 0) || (index > _colourList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.Colour) _colourList.elementAt(index); - } //-- jalview.binding.Colour getColour(int) + } //-- jalview.binding.Colour getColour(int) /** * Method getColour - * - * - * + * + * + * * @return Colour */ public jalview.binding.Colour[] getColour() @@ -128,25 +147,25 @@ public class JalviewUserColours implements java.io.Serializable { mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index); } return mArray; - } //-- jalview.binding.Colour[] getColour() + } //-- jalview.binding.Colour[] getColour() /** * Method getColourCount - * - * - * + * + * + * * @return int */ public int getColourCount() { return _colourList.size(); - } //-- int getColourCount() + } //-- int getColourCount() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -158,50 +177,50 @@ public class JalviewUserColours implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllColour - * + * */ public void removeAllColour() { _colourList.removeAllElements(); - } //-- void removeAllColour() + } //-- void removeAllColour() /** * Method removeColour - * - * - * + * + * + * * @param index * @return Colour */ @@ -210,13 +229,13 @@ public class JalviewUserColours implements java.io.Serializable { java.lang.Object obj = _colourList.elementAt(index); _colourList.removeElementAt(index); return (jalview.binding.Colour) obj; - } //-- jalview.binding.Colour removeColour(int) + } //-- jalview.binding.Colour removeColour(int) /** * Method setColour - * - * - * + * + * + * * @param index * @param vColour */ @@ -228,13 +247,13 @@ public class JalviewUserColours implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _colourList.setElementAt(vColour, index); - } //-- void setColour(int, jalview.binding.Colour) + } //-- void setColour(int, jalview.binding.Colour) /** * Method setColour - * - * - * + * + * + * * @param colourArray */ public void setColour(jalview.binding.Colour[] colourArray) @@ -244,13 +263,13 @@ public class JalviewUserColours implements java.io.Serializable { for (int i = 0; i < colourArray.length; i++) { _colourList.addElement(colourArray[i]); } - } //-- void setColour(jalview.binding.Colour) + } //-- void setColour(jalview.binding.Colour) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -258,17 +277,17 @@ public class JalviewUserColours implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/JalviewUserColoursItem.java b/src/jalview/binding/JalviewUserColoursItem.java index ce6919c..b7abdc5 100755 --- a/src/jalview/binding/JalviewUserColoursItem.java +++ b/src/jalview/binding/JalviewUserColoursItem.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -17,7 +36,7 @@ import org.exolab.castor.xml.Unmarshaller; /** * Class JalviewUserColoursItem. - * + * * @version $Revision$ $Date$ */ public class JalviewUserColoursItem implements java.io.Serializable { @@ -48,23 +67,23 @@ public class JalviewUserColoursItem implements java.io.Serializable { /** * Returns the value of field 'colour'. - * + * * @return Colour * @return the value of field 'colour'. */ public jalview.binding.Colour getColour() { return this._colour; - } //-- jalview.binding.Colour getColour() + } //-- jalview.binding.Colour getColour() /** * Sets the value of field 'colour'. - * + * * @param colour the value of field 'colour'. */ public void setColour(jalview.binding.Colour colour) { this._colour = colour; - } //-- void setColour(jalview.binding.Colour) + } //-- void setColour(jalview.binding.Colour) } diff --git a/src/jalview/binding/Residue.java b/src/jalview/binding/Residue.java index 69e4312..9e68130 100755 --- a/src/jalview/binding/Residue.java +++ b/src/jalview/binding/Residue.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,7 +42,7 @@ import org.xml.sax.ContentHandler; /** * Class Residue. - * + * * @version $Revision$ $Date$ */ public class Residue implements java.io.Serializable { @@ -64,52 +83,52 @@ public class Residue implements java.io.Serializable { /** * Method deleteRGB - * + * */ public void deleteRGB() { this._has_RGB= false; - } //-- void deleteRGB() + } //-- void deleteRGB() /** * Returns the value of field 'name'. - * + * * @return String * @return the value of field 'name'. */ public java.lang.String getName() { return this._name; - } //-- java.lang.String getName() + } //-- java.lang.String getName() /** * Returns the value of field 'RGB'. - * + * * @return int * @return the value of field 'RGB'. */ public int getRGB() { return this._RGB; - } //-- int getRGB() + } //-- int getRGB() /** * Method hasRGB - * - * - * + * + * + * * @return boolean */ public boolean hasRGB() { return this._has_RGB; - } //-- boolean hasRGB() + } //-- boolean hasRGB() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -121,62 +140,62 @@ public class Residue implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'name'. - * + * * @param name the value of field 'name'. */ public void setName(java.lang.String name) { this._name = name; - } //-- void setName(java.lang.String) + } //-- void setName(java.lang.String) /** * Sets the value of field 'RGB'. - * + * * @param RGB the value of field 'RGB'. */ public void setRGB(int RGB) { this._RGB = RGB; this._has_RGB = true; - } //-- void setRGB(int) + } //-- void setRGB(int) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -184,17 +203,17 @@ public class Residue implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.Residue) Unmarshaller.unmarshal(jalview.binding.Residue.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java index f3fd4e4..290354e 100755 --- a/src/jalview/binding/Sequence.java +++ b/src/jalview/binding/Sequence.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,10 +42,10 @@ import org.xml.sax.ContentHandler; /** * Class Sequence. - * + * * @version $Revision$ $Date$ */ -public class Sequence extends SequenceType +public class Sequence extends SequenceType implements java.io.Serializable { @@ -46,9 +65,9 @@ implements java.io.Serializable /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -60,41 +79,41 @@ implements java.io.Serializable return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -102,17 +121,17 @@ implements java.io.Serializable throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java index 7ed3b52..7ef5fe7 100755 --- a/src/jalview/binding/SequenceSet.java +++ b/src/jalview/binding/SequenceSet.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -25,7 +44,7 @@ import org.xml.sax.ContentHandler; /** * Class SequenceSet. - * + * * @version $Revision$ $Date$ */ public class SequenceSet implements java.io.Serializable { @@ -78,22 +97,22 @@ public class SequenceSet implements java.io.Serializable { /** * Method addAnnotation - * - * - * + * + * + * * @param vAnnotation */ public void addAnnotation(jalview.binding.Annotation vAnnotation) throws java.lang.IndexOutOfBoundsException { _annotationList.addElement(vAnnotation); - } //-- void addAnnotation(jalview.binding.Annotation) + } //-- void addAnnotation(jalview.binding.Annotation) /** * Method addAnnotation - * - * - * + * + * + * * @param index * @param vAnnotation */ @@ -101,26 +120,26 @@ public class SequenceSet implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _annotationList.insertElementAt(vAnnotation, index); - } //-- void addAnnotation(int, jalview.binding.Annotation) + } //-- void addAnnotation(int, jalview.binding.Annotation) /** * Method addSequence - * - * - * + * + * + * * @param vSequence */ public void addSequence(jalview.binding.Sequence vSequence) throws java.lang.IndexOutOfBoundsException { _sequenceList.addElement(vSequence); - } //-- void addSequence(jalview.binding.Sequence) + } //-- void addSequence(jalview.binding.Sequence) /** * Method addSequence - * - * - * + * + * + * * @param index * @param vSequence */ @@ -128,57 +147,57 @@ public class SequenceSet implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _sequenceList.insertElementAt(vSequence, index); - } //-- void addSequence(int, jalview.binding.Sequence) + } //-- void addSequence(int, jalview.binding.Sequence) /** * Method deleteAligned - * + * */ public void deleteAligned() { this._has_aligned= false; - } //-- void deleteAligned() + } //-- void deleteAligned() /** * Method enumerateAnnotation - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateAnnotation() { return _annotationList.elements(); - } //-- java.util.Enumeration enumerateAnnotation() + } //-- java.util.Enumeration enumerateAnnotation() /** * Method enumerateSequence - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateSequence() { return _sequenceList.elements(); - } //-- java.util.Enumeration enumerateSequence() + } //-- java.util.Enumeration enumerateSequence() /** * Returns the value of field 'aligned'. - * + * * @return boolean * @return the value of field 'aligned'. */ public boolean getAligned() { return this._aligned; - } //-- boolean getAligned() + } //-- boolean getAligned() /** * Method getAnnotation - * - * - * + * + * + * * @param index * @return Annotation */ @@ -189,15 +208,15 @@ public class SequenceSet implements java.io.Serializable { if ((index < 0) || (index > _annotationList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.Annotation) _annotationList.elementAt(index); - } //-- jalview.binding.Annotation getAnnotation(int) + } //-- jalview.binding.Annotation getAnnotation(int) /** * Method getAnnotation - * - * - * + * + * + * * @return Annotation */ public jalview.binding.Annotation[] getAnnotation() @@ -208,36 +227,36 @@ public class SequenceSet implements java.io.Serializable { mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index); } return mArray; - } //-- jalview.binding.Annotation[] getAnnotation() + } //-- jalview.binding.Annotation[] getAnnotation() /** * Method getAnnotationCount - * - * - * + * + * + * * @return int */ public int getAnnotationCount() { return _annotationList.size(); - } //-- int getAnnotationCount() + } //-- int getAnnotationCount() /** * Returns the value of field 'gapChar'. - * + * * @return String * @return the value of field 'gapChar'. */ public java.lang.String getGapChar() { return this._gapChar; - } //-- java.lang.String getGapChar() + } //-- java.lang.String getGapChar() /** * Method getSequence - * - * - * + * + * + * * @param index * @return Sequence */ @@ -248,15 +267,15 @@ public class SequenceSet implements java.io.Serializable { if ((index < 0) || (index > _sequenceList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.Sequence) _sequenceList.elementAt(index); - } //-- jalview.binding.Sequence getSequence(int) + } //-- jalview.binding.Sequence getSequence(int) /** * Method getSequence - * - * - * + * + * + * * @return Sequence */ public jalview.binding.Sequence[] getSequence() @@ -267,37 +286,37 @@ public class SequenceSet implements java.io.Serializable { mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index); } return mArray; - } //-- jalview.binding.Sequence[] getSequence() + } //-- jalview.binding.Sequence[] getSequence() /** * Method getSequenceCount - * - * - * + * + * + * * @return int */ public int getSequenceCount() { return _sequenceList.size(); - } //-- int getSequenceCount() + } //-- int getSequenceCount() /** * Method hasAligned - * - * - * + * + * + * * @return boolean */ public boolean hasAligned() { return this._has_aligned; - } //-- boolean hasAligned() + } //-- boolean hasAligned() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -309,59 +328,59 @@ public class SequenceSet implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllAnnotation - * + * */ public void removeAllAnnotation() { _annotationList.removeAllElements(); - } //-- void removeAllAnnotation() + } //-- void removeAllAnnotation() /** * Method removeAllSequence - * + * */ public void removeAllSequence() { _sequenceList.removeAllElements(); - } //-- void removeAllSequence() + } //-- void removeAllSequence() /** * Method removeAnnotation - * - * - * + * + * + * * @param index * @return Annotation */ @@ -370,13 +389,13 @@ public class SequenceSet implements java.io.Serializable { java.lang.Object obj = _annotationList.elementAt(index); _annotationList.removeElementAt(index); return (jalview.binding.Annotation) obj; - } //-- jalview.binding.Annotation removeAnnotation(int) + } //-- jalview.binding.Annotation removeAnnotation(int) /** * Method removeSequence - * - * - * + * + * + * * @param index * @return Sequence */ @@ -385,24 +404,24 @@ public class SequenceSet implements java.io.Serializable { java.lang.Object obj = _sequenceList.elementAt(index); _sequenceList.removeElementAt(index); return (jalview.binding.Sequence) obj; - } //-- jalview.binding.Sequence removeSequence(int) + } //-- jalview.binding.Sequence removeSequence(int) /** * Sets the value of field 'aligned'. - * + * * @param aligned the value of field 'aligned'. */ public void setAligned(boolean aligned) { this._aligned = aligned; this._has_aligned = true; - } //-- void setAligned(boolean) + } //-- void setAligned(boolean) /** * Method setAnnotation - * - * - * + * + * + * * @param index * @param vAnnotation */ @@ -414,13 +433,13 @@ public class SequenceSet implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _annotationList.setElementAt(vAnnotation, index); - } //-- void setAnnotation(int, jalview.binding.Annotation) + } //-- void setAnnotation(int, jalview.binding.Annotation) /** * Method setAnnotation - * - * - * + * + * + * * @param annotationArray */ public void setAnnotation(jalview.binding.Annotation[] annotationArray) @@ -430,23 +449,23 @@ public class SequenceSet implements java.io.Serializable { for (int i = 0; i < annotationArray.length; i++) { _annotationList.addElement(annotationArray[i]); } - } //-- void setAnnotation(jalview.binding.Annotation) + } //-- void setAnnotation(jalview.binding.Annotation) /** * Sets the value of field 'gapChar'. - * + * * @param gapChar the value of field 'gapChar'. */ public void setGapChar(java.lang.String gapChar) { this._gapChar = gapChar; - } //-- void setGapChar(java.lang.String) + } //-- void setGapChar(java.lang.String) /** * Method setSequence - * - * - * + * + * + * * @param index * @param vSequence */ @@ -458,13 +477,13 @@ public class SequenceSet implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _sequenceList.setElementAt(vSequence, index); - } //-- void setSequence(int, jalview.binding.Sequence) + } //-- void setSequence(int, jalview.binding.Sequence) /** * Method setSequence - * - * - * + * + * + * * @param sequenceArray */ public void setSequence(jalview.binding.Sequence[] sequenceArray) @@ -474,13 +493,13 @@ public class SequenceSet implements java.io.Serializable { for (int i = 0; i < sequenceArray.length; i++) { _sequenceList.addElement(sequenceArray[i]); } - } //-- void setSequence(jalview.binding.Sequence) + } //-- void setSequence(jalview.binding.Sequence) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -488,17 +507,17 @@ public class SequenceSet implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java index 3a935e4..bf560bb 100755 --- a/src/jalview/binding/SequenceType.java +++ b/src/jalview/binding/SequenceType.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,7 +42,7 @@ import org.xml.sax.ContentHandler; /** * Class SequenceType. - * + * * @version $Revision$ $Date$ */ public class SequenceType implements java.io.Serializable { @@ -64,42 +83,42 @@ public class SequenceType implements java.io.Serializable { /** * Returns the value of field 'id'. - * + * * @return String * @return the value of field 'id'. */ public java.lang.String getId() { return this._id; - } //-- java.lang.String getId() + } //-- java.lang.String getId() /** * Returns the value of field 'name'. - * + * * @return String * @return the value of field 'name'. */ public java.lang.String getName() { return this._name; - } //-- java.lang.String getName() + } //-- java.lang.String getName() /** * Returns the value of field 'sequence'. - * + * * @return String * @return the value of field 'sequence'. */ public java.lang.String getSequence() { return this._sequence; - } //-- java.lang.String getSequence() + } //-- java.lang.String getSequence() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -111,71 +130,71 @@ public class SequenceType implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'id'. - * + * * @param id the value of field 'id'. */ public void setId(java.lang.String id) { this._id = id; - } //-- void setId(java.lang.String) + } //-- void setId(java.lang.String) /** * Sets the value of field 'name'. - * + * * @param name the value of field 'name'. */ public void setName(java.lang.String name) { this._name = name; - } //-- void setName(java.lang.String) + } //-- void setName(java.lang.String) /** * Sets the value of field 'sequence'. - * + * * @param sequence the value of field 'sequence'. */ public void setSequence(java.lang.String sequence) { this._sequence = sequence; - } //-- void setSequence(java.lang.String) + } //-- void setSequence(java.lang.String) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -183,17 +202,17 @@ public class SequenceType implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/UserColour.java b/src/jalview/binding/UserColour.java index 837d9af..fba081c 100755 --- a/src/jalview/binding/UserColour.java +++ b/src/jalview/binding/UserColour.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,7 +42,7 @@ import org.xml.sax.ContentHandler; /** * Class UserColour. - * + * * @version $Revision$ $Date$ */ public class UserColour implements java.io.Serializable { @@ -64,52 +83,52 @@ public class UserColour implements java.io.Serializable { /** * Method deleteId - * + * */ public void deleteId() { this._has_id= false; - } //-- void deleteId() + } //-- void deleteId() /** * Returns the value of field 'id'. - * + * * @return int * @return the value of field 'id'. */ public int getId() { return this._id; - } //-- int getId() + } //-- int getId() /** * Returns the value of field 'userColourScheme'. - * + * * @return UserColourScheme * @return the value of field 'userColourScheme'. */ public jalview.binding.UserColourScheme getUserColourScheme() { return this._userColourScheme; - } //-- jalview.binding.UserColourScheme getUserColourScheme() + } //-- jalview.binding.UserColourScheme getUserColourScheme() /** * Method hasId - * - * - * + * + * + * * @return boolean */ public boolean hasId() { return this._has_id; - } //-- boolean hasId() + } //-- boolean hasId() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -121,62 +140,62 @@ public class UserColour implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'id'. - * + * * @param id the value of field 'id'. */ public void setId(int id) { this._id = id; this._has_id = true; - } //-- void setId(int) + } //-- void setId(int) /** * Sets the value of field 'userColourScheme'. - * + * * @param userColourScheme the value of field 'userColourScheme' */ public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme) { this._userColourScheme = userColourScheme; - } //-- void setUserColourScheme(jalview.binding.UserColourScheme) + } //-- void setUserColourScheme(jalview.binding.UserColourScheme) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -184,17 +203,17 @@ public class UserColour implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.UserColour) Unmarshaller.unmarshal(jalview.binding.UserColour.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java index 79ea637..f8c2fdb 100755 --- a/src/jalview/binding/UserColourScheme.java +++ b/src/jalview/binding/UserColourScheme.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,10 +42,10 @@ import org.xml.sax.ContentHandler; /** * Class UserColourScheme. - * + * * @version $Revision$ $Date$ */ -public class UserColourScheme extends JalviewUserColours +public class UserColourScheme extends JalviewUserColours implements java.io.Serializable { @@ -46,9 +65,9 @@ implements java.io.Serializable /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -60,41 +79,41 @@ implements java.io.Serializable return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -102,17 +121,17 @@ implements java.io.Serializable throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java index 241aaab..2c4e91b 100755 --- a/src/jalview/binding/UserColours.java +++ b/src/jalview/binding/UserColours.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,7 +42,7 @@ import org.xml.sax.ContentHandler; /** * Class UserColours. - * + * * @version $Revision$ $Date$ */ public class UserColours implements java.io.Serializable { @@ -59,31 +78,31 @@ public class UserColours implements java.io.Serializable { /** * Returns the value of field 'id'. - * + * * @return String * @return the value of field 'id'. */ public java.lang.String getId() { return this._id; - } //-- java.lang.String getId() + } //-- java.lang.String getId() /** * Returns the value of field 'userColourScheme'. - * + * * @return UserColourScheme * @return the value of field 'userColourScheme'. */ public jalview.binding.UserColourScheme getUserColourScheme() { return this._userColourScheme; - } //-- jalview.binding.UserColourScheme getUserColourScheme() + } //-- jalview.binding.UserColourScheme getUserColourScheme() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -95,61 +114,61 @@ public class UserColours implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'id'. - * + * * @param id the value of field 'id'. */ public void setId(java.lang.String id) { this._id = id; - } //-- void setId(java.lang.String) + } //-- void setId(java.lang.String) /** * Sets the value of field 'userColourScheme'. - * + * * @param userColourScheme the value of field 'userColourScheme' */ public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme) { this._userColourScheme = userColourScheme; - } //-- void setUserColourScheme(jalview.binding.UserColourScheme) + } //-- void setUserColourScheme(jalview.binding.UserColourScheme) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -157,17 +176,17 @@ public class UserColours implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java index b4237b8..2190b2f 100755 --- a/src/jalview/binding/VAMSAS.java +++ b/src/jalview/binding/VAMSAS.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -25,7 +44,7 @@ import org.xml.sax.ContentHandler; /** * Class VAMSAS. - * + * * @version $Revision$ $Date$ */ public class VAMSAS implements java.io.Serializable { @@ -69,22 +88,22 @@ public class VAMSAS implements java.io.Serializable { /** * Method addAlignment - * - * - * + * + * + * * @param vAlignment */ public void addAlignment(jalview.binding.Alignment vAlignment) throws java.lang.IndexOutOfBoundsException { _alignmentList.addElement(vAlignment); - } //-- void addAlignment(jalview.binding.Alignment) + } //-- void addAlignment(jalview.binding.Alignment) /** * Method addAlignment - * - * - * + * + * + * * @param index * @param vAlignment */ @@ -92,26 +111,26 @@ public class VAMSAS implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _alignmentList.insertElementAt(vAlignment, index); - } //-- void addAlignment(int, jalview.binding.Alignment) + } //-- void addAlignment(int, jalview.binding.Alignment) /** * Method addSequenceSet - * - * - * + * + * + * * @param vSequenceSet */ public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet) throws java.lang.IndexOutOfBoundsException { _sequenceSetList.addElement(vSequenceSet); - } //-- void addSequenceSet(jalview.binding.SequenceSet) + } //-- void addSequenceSet(jalview.binding.SequenceSet) /** * Method addSequenceSet - * - * - * + * + * + * * @param index * @param vSequenceSet */ @@ -119,26 +138,26 @@ public class VAMSAS implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _sequenceSetList.insertElementAt(vSequenceSet, index); - } //-- void addSequenceSet(int, jalview.binding.SequenceSet) + } //-- void addSequenceSet(int, jalview.binding.SequenceSet) /** * Method addTree - * - * - * + * + * + * * @param vTree */ public void addTree(java.lang.String vTree) throws java.lang.IndexOutOfBoundsException { _treeList.addElement(vTree); - } //-- void addTree(java.lang.String) + } //-- void addTree(java.lang.String) /** * Method addTree - * - * - * + * + * + * * @param index * @param vTree */ @@ -146,49 +165,49 @@ public class VAMSAS implements java.io.Serializable { throws java.lang.IndexOutOfBoundsException { _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, java.lang.String) + } //-- void addTree(int, java.lang.String) /** * Method enumerateAlignment - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateAlignment() { return _alignmentList.elements(); - } //-- java.util.Enumeration enumerateAlignment() + } //-- java.util.Enumeration enumerateAlignment() /** * Method enumerateSequenceSet - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateSequenceSet() { return _sequenceSetList.elements(); - } //-- java.util.Enumeration enumerateSequenceSet() + } //-- java.util.Enumeration enumerateSequenceSet() /** * Method enumerateTree - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateTree() { return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() + } //-- java.util.Enumeration enumerateTree() /** * Method getAlignment - * - * - * + * + * + * * @param index * @return Alignment */ @@ -199,15 +218,15 @@ public class VAMSAS implements java.io.Serializable { if ((index < 0) || (index > _alignmentList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.Alignment) _alignmentList.elementAt(index); - } //-- jalview.binding.Alignment getAlignment(int) + } //-- jalview.binding.Alignment getAlignment(int) /** * Method getAlignment - * - * - * + * + * + * * @return Alignment */ public jalview.binding.Alignment[] getAlignment() @@ -218,25 +237,25 @@ public class VAMSAS implements java.io.Serializable { mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index); } return mArray; - } //-- jalview.binding.Alignment[] getAlignment() + } //-- jalview.binding.Alignment[] getAlignment() /** * Method getAlignmentCount - * - * - * + * + * + * * @return int */ public int getAlignmentCount() { return _alignmentList.size(); - } //-- int getAlignmentCount() + } //-- int getAlignmentCount() /** * Method getSequenceSet - * - * - * + * + * + * * @param index * @return SequenceSet */ @@ -247,15 +266,15 @@ public class VAMSAS implements java.io.Serializable { if ((index < 0) || (index > _sequenceSetList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index); - } //-- jalview.binding.SequenceSet getSequenceSet(int) + } //-- jalview.binding.SequenceSet getSequenceSet(int) /** * Method getSequenceSet - * - * - * + * + * + * * @return SequenceSet */ public jalview.binding.SequenceSet[] getSequenceSet() @@ -266,25 +285,25 @@ public class VAMSAS implements java.io.Serializable { mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index); } return mArray; - } //-- jalview.binding.SequenceSet[] getSequenceSet() + } //-- jalview.binding.SequenceSet[] getSequenceSet() /** * Method getSequenceSetCount - * - * - * + * + * + * * @return int */ public int getSequenceSetCount() { return _sequenceSetList.size(); - } //-- int getSequenceSetCount() + } //-- int getSequenceSetCount() /** * Method getTree - * - * - * + * + * + * * @param index * @return String */ @@ -295,15 +314,15 @@ public class VAMSAS implements java.io.Serializable { if ((index < 0) || (index > _treeList.size())) { throw new IndexOutOfBoundsException(); } - + return (String)_treeList.elementAt(index); - } //-- java.lang.String getTree(int) + } //-- java.lang.String getTree(int) /** * Method getTree - * - * - * + * + * + * * @return String */ public java.lang.String[] getTree() @@ -314,25 +333,25 @@ public class VAMSAS implements java.io.Serializable { mArray[index] = (String)_treeList.elementAt(index); } return mArray; - } //-- java.lang.String[] getTree() + } //-- java.lang.String[] getTree() /** * Method getTreeCount - * - * - * + * + * + * * @return int */ public int getTreeCount() { return _treeList.size(); - } //-- int getTreeCount() + } //-- int getTreeCount() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -344,41 +363,41 @@ public class VAMSAS implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAlignment - * - * - * + * + * + * * @param index * @return Alignment */ @@ -387,40 +406,40 @@ public class VAMSAS implements java.io.Serializable { java.lang.Object obj = _alignmentList.elementAt(index); _alignmentList.removeElementAt(index); return (jalview.binding.Alignment) obj; - } //-- jalview.binding.Alignment removeAlignment(int) + } //-- jalview.binding.Alignment removeAlignment(int) /** * Method removeAllAlignment - * + * */ public void removeAllAlignment() { _alignmentList.removeAllElements(); - } //-- void removeAllAlignment() + } //-- void removeAllAlignment() /** * Method removeAllSequenceSet - * + * */ public void removeAllSequenceSet() { _sequenceSetList.removeAllElements(); - } //-- void removeAllSequenceSet() + } //-- void removeAllSequenceSet() /** * Method removeAllTree - * + * */ public void removeAllTree() { _treeList.removeAllElements(); - } //-- void removeAllTree() + } //-- void removeAllTree() /** * Method removeSequenceSet - * - * - * + * + * + * * @param index * @return SequenceSet */ @@ -429,13 +448,13 @@ public class VAMSAS implements java.io.Serializable { java.lang.Object obj = _sequenceSetList.elementAt(index); _sequenceSetList.removeElementAt(index); return (jalview.binding.SequenceSet) obj; - } //-- jalview.binding.SequenceSet removeSequenceSet(int) + } //-- jalview.binding.SequenceSet removeSequenceSet(int) /** * Method removeTree - * - * - * + * + * + * * @param index * @return String */ @@ -444,13 +463,13 @@ public class VAMSAS implements java.io.Serializable { java.lang.Object obj = _treeList.elementAt(index); _treeList.removeElementAt(index); return (String)obj; - } //-- java.lang.String removeTree(int) + } //-- java.lang.String removeTree(int) /** * Method setAlignment - * - * - * + * + * + * * @param index * @param vAlignment */ @@ -462,13 +481,13 @@ public class VAMSAS implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _alignmentList.setElementAt(vAlignment, index); - } //-- void setAlignment(int, jalview.binding.Alignment) + } //-- void setAlignment(int, jalview.binding.Alignment) /** * Method setAlignment - * - * - * + * + * + * * @param alignmentArray */ public void setAlignment(jalview.binding.Alignment[] alignmentArray) @@ -478,13 +497,13 @@ public class VAMSAS implements java.io.Serializable { for (int i = 0; i < alignmentArray.length; i++) { _alignmentList.addElement(alignmentArray[i]); } - } //-- void setAlignment(jalview.binding.Alignment) + } //-- void setAlignment(jalview.binding.Alignment) /** * Method setSequenceSet - * - * - * + * + * + * * @param index * @param vSequenceSet */ @@ -496,13 +515,13 @@ public class VAMSAS implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _sequenceSetList.setElementAt(vSequenceSet, index); - } //-- void setSequenceSet(int, jalview.binding.SequenceSet) + } //-- void setSequenceSet(int, jalview.binding.SequenceSet) /** * Method setSequenceSet - * - * - * + * + * + * * @param sequenceSetArray */ public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray) @@ -512,13 +531,13 @@ public class VAMSAS implements java.io.Serializable { for (int i = 0; i < sequenceSetArray.length; i++) { _sequenceSetList.addElement(sequenceSetArray[i]); } - } //-- void setSequenceSet(jalview.binding.SequenceSet) + } //-- void setSequenceSet(jalview.binding.SequenceSet) /** * Method setTree - * - * - * + * + * + * * @param index * @param vTree */ @@ -530,13 +549,13 @@ public class VAMSAS implements java.io.Serializable { throw new IndexOutOfBoundsException(); } _treeList.setElementAt(vTree, index); - } //-- void setTree(int, java.lang.String) + } //-- void setTree(int, java.lang.String) /** * Method setTree - * - * - * + * + * + * * @param treeArray */ public void setTree(java.lang.String[] treeArray) @@ -546,13 +565,13 @@ public class VAMSAS implements java.io.Serializable { for (int i = 0; i < treeArray.length; i++) { _treeList.addElement(treeArray[i]); } - } //-- void setTree(java.lang.String) + } //-- void setTree(java.lang.String) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -560,17 +579,17 @@ public class VAMSAS implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java index a4d4362..4133b84 100755 --- a/src/jalview/binding/VamsasModel.java +++ b/src/jalview/binding/VamsasModel.java @@ -1,10 +1,29 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.binding; //---------------------------------/ @@ -23,10 +42,10 @@ import org.xml.sax.ContentHandler; /** * Class VamsasModel. - * + * * @version $Revision$ $Date$ */ -public class VamsasModel extends VAMSAS +public class VamsasModel extends VAMSAS implements java.io.Serializable { @@ -46,9 +65,9 @@ implements java.io.Serializable /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -60,41 +79,41 @@ implements java.io.Serializable return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -102,17 +121,17 @@ implements java.io.Serializable throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java index 911061b..99dbd1b 100755 --- a/src/jalview/binding/Viewport.java +++ b/src/jalview/binding/Viewport.java @@ -1,10 +1,30 @@ /* - * This class was automatically generated with +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + +/* + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ + package jalview.binding; //---------------------------------/ @@ -23,7 +43,7 @@ import org.xml.sax.ContentHandler; /** * Class Viewport. - * + * * @version $Revision$ $Date$ */ public class Viewport implements java.io.Serializable { @@ -294,778 +314,778 @@ public class Viewport implements java.io.Serializable { /** * Method deleteConsThreshold - * + * */ public void deleteConsThreshold() { this._has_consThreshold= false; - } //-- void deleteConsThreshold() + } //-- void deleteConsThreshold() /** * Method deleteConservationSelected - * + * */ public void deleteConservationSelected() { this._has_conservationSelected= false; - } //-- void deleteConservationSelected() + } //-- void deleteConservationSelected() /** * Method deleteFontSize - * + * */ public void deleteFontSize() { this._has_fontSize= false; - } //-- void deleteFontSize() + } //-- void deleteFontSize() /** * Method deleteFontStyle - * + * */ public void deleteFontStyle() { this._has_fontStyle= false; - } //-- void deleteFontStyle() + } //-- void deleteFontStyle() /** * Method deleteHeight - * + * */ public void deleteHeight() { this._has_height= false; - } //-- void deleteHeight() + } //-- void deleteHeight() /** * Method deletePidSelected - * + * */ public void deletePidSelected() { this._has_pidSelected= false; - } //-- void deletePidSelected() + } //-- void deletePidSelected() /** * Method deletePidThreshold - * + * */ public void deletePidThreshold() { this._has_pidThreshold= false; - } //-- void deletePidThreshold() + } //-- void deletePidThreshold() /** * Method deleteRenderGaps - * + * */ public void deleteRenderGaps() { this._has_renderGaps= false; - } //-- void deleteRenderGaps() + } //-- void deleteRenderGaps() /** * Method deleteShowAnnotation - * + * */ public void deleteShowAnnotation() { this._has_showAnnotation= false; - } //-- void deleteShowAnnotation() + } //-- void deleteShowAnnotation() /** * Method deleteShowBoxes - * + * */ public void deleteShowBoxes() { this._has_showBoxes= false; - } //-- void deleteShowBoxes() + } //-- void deleteShowBoxes() /** * Method deleteShowColourText - * + * */ public void deleteShowColourText() { this._has_showColourText= false; - } //-- void deleteShowColourText() + } //-- void deleteShowColourText() /** * Method deleteShowConservation - * + * */ public void deleteShowConservation() { this._has_showConservation= false; - } //-- void deleteShowConservation() + } //-- void deleteShowConservation() /** * Method deleteShowFullId - * + * */ public void deleteShowFullId() { this._has_showFullId= false; - } //-- void deleteShowFullId() + } //-- void deleteShowFullId() /** * Method deleteShowIdentity - * + * */ public void deleteShowIdentity() { this._has_showIdentity= false; - } //-- void deleteShowIdentity() + } //-- void deleteShowIdentity() /** * Method deleteShowQuality - * + * */ public void deleteShowQuality() { this._has_showQuality= false; - } //-- void deleteShowQuality() + } //-- void deleteShowQuality() /** * Method deleteShowSequenceFeatures - * + * */ public void deleteShowSequenceFeatures() { this._has_showSequenceFeatures= false; - } //-- void deleteShowSequenceFeatures() + } //-- void deleteShowSequenceFeatures() /** * Method deleteShowText - * + * */ public void deleteShowText() { this._has_showText= false; - } //-- void deleteShowText() + } //-- void deleteShowText() /** * Method deleteStartRes - * + * */ public void deleteStartRes() { this._has_startRes= false; - } //-- void deleteStartRes() + } //-- void deleteStartRes() /** * Method deleteStartSeq - * + * */ public void deleteStartSeq() { this._has_startSeq= false; - } //-- void deleteStartSeq() + } //-- void deleteStartSeq() /** * Method deleteWidth - * + * */ public void deleteWidth() { this._has_width= false; - } //-- void deleteWidth() + } //-- void deleteWidth() /** * Method deleteWrapAlignment - * + * */ public void deleteWrapAlignment() { this._has_wrapAlignment= false; - } //-- void deleteWrapAlignment() + } //-- void deleteWrapAlignment() /** * Method deleteXpos - * + * */ public void deleteXpos() { this._has_xpos= false; - } //-- void deleteXpos() + } //-- void deleteXpos() /** * Method deleteYpos - * + * */ public void deleteYpos() { this._has_ypos= false; - } //-- void deleteYpos() + } //-- void deleteYpos() /** * Returns the value of field 'bgColour'. - * + * * @return String * @return the value of field 'bgColour'. */ public java.lang.String getBgColour() { return this._bgColour; - } //-- java.lang.String getBgColour() + } //-- java.lang.String getBgColour() /** * Returns the value of field 'consThreshold'. - * + * * @return int * @return the value of field 'consThreshold'. */ public int getConsThreshold() { return this._consThreshold; - } //-- int getConsThreshold() + } //-- int getConsThreshold() /** * Returns the value of field 'conservationSelected'. - * + * * @return boolean * @return the value of field 'conservationSelected'. */ public boolean getConservationSelected() { return this._conservationSelected; - } //-- boolean getConservationSelected() + } //-- boolean getConservationSelected() /** * Returns the value of field 'fontName'. - * + * * @return String * @return the value of field 'fontName'. */ public java.lang.String getFontName() { return this._fontName; - } //-- java.lang.String getFontName() + } //-- java.lang.String getFontName() /** * Returns the value of field 'fontSize'. - * + * * @return int * @return the value of field 'fontSize'. */ public int getFontSize() { return this._fontSize; - } //-- int getFontSize() + } //-- int getFontSize() /** * Returns the value of field 'fontStyle'. - * + * * @return int * @return the value of field 'fontStyle'. */ public int getFontStyle() { return this._fontStyle; - } //-- int getFontStyle() + } //-- int getFontStyle() /** * Returns the value of field 'height'. - * + * * @return int * @return the value of field 'height'. */ public int getHeight() { return this._height; - } //-- int getHeight() + } //-- int getHeight() /** * Returns the value of field 'pidSelected'. - * + * * @return boolean * @return the value of field 'pidSelected'. */ public boolean getPidSelected() { return this._pidSelected; - } //-- boolean getPidSelected() + } //-- boolean getPidSelected() /** * Returns the value of field 'pidThreshold'. - * + * * @return int * @return the value of field 'pidThreshold'. */ public int getPidThreshold() { return this._pidThreshold; - } //-- int getPidThreshold() + } //-- int getPidThreshold() /** * Returns the value of field 'renderGaps'. - * + * * @return boolean * @return the value of field 'renderGaps'. */ public boolean getRenderGaps() { return this._renderGaps; - } //-- boolean getRenderGaps() + } //-- boolean getRenderGaps() /** * Returns the value of field 'showAnnotation'. - * + * * @return boolean * @return the value of field 'showAnnotation'. */ public boolean getShowAnnotation() { return this._showAnnotation; - } //-- boolean getShowAnnotation() + } //-- boolean getShowAnnotation() /** * Returns the value of field 'showBoxes'. - * + * * @return boolean * @return the value of field 'showBoxes'. */ public boolean getShowBoxes() { return this._showBoxes; - } //-- boolean getShowBoxes() + } //-- boolean getShowBoxes() /** * Returns the value of field 'showColourText'. - * + * * @return boolean * @return the value of field 'showColourText'. */ public boolean getShowColourText() { return this._showColourText; - } //-- boolean getShowColourText() + } //-- boolean getShowColourText() /** * Returns the value of field 'showConservation'. - * + * * @return boolean * @return the value of field 'showConservation'. */ public boolean getShowConservation() { return this._showConservation; - } //-- boolean getShowConservation() + } //-- boolean getShowConservation() /** * Returns the value of field 'showFullId'. - * + * * @return boolean * @return the value of field 'showFullId'. */ public boolean getShowFullId() { return this._showFullId; - } //-- boolean getShowFullId() + } //-- boolean getShowFullId() /** * Returns the value of field 'showIdentity'. - * + * * @return boolean * @return the value of field 'showIdentity'. */ public boolean getShowIdentity() { return this._showIdentity; - } //-- boolean getShowIdentity() + } //-- boolean getShowIdentity() /** * Returns the value of field 'showQuality'. - * + * * @return boolean * @return the value of field 'showQuality'. */ public boolean getShowQuality() { return this._showQuality; - } //-- boolean getShowQuality() + } //-- boolean getShowQuality() /** * Returns the value of field 'showSequenceFeatures'. - * + * * @return boolean * @return the value of field 'showSequenceFeatures'. */ public boolean getShowSequenceFeatures() { return this._showSequenceFeatures; - } //-- boolean getShowSequenceFeatures() + } //-- boolean getShowSequenceFeatures() /** * Returns the value of field 'showText'. - * + * * @return boolean * @return the value of field 'showText'. */ public boolean getShowText() { return this._showText; - } //-- boolean getShowText() + } //-- boolean getShowText() /** * Returns the value of field 'startRes'. - * + * * @return int * @return the value of field 'startRes'. */ public int getStartRes() { return this._startRes; - } //-- int getStartRes() + } //-- int getStartRes() /** * Returns the value of field 'startSeq'. - * + * * @return int * @return the value of field 'startSeq'. */ public int getStartSeq() { return this._startSeq; - } //-- int getStartSeq() + } //-- int getStartSeq() /** * Returns the value of field 'title'. - * + * * @return String * @return the value of field 'title'. */ public java.lang.String getTitle() { return this._title; - } //-- java.lang.String getTitle() + } //-- java.lang.String getTitle() /** * Returns the value of field 'width'. - * + * * @return int * @return the value of field 'width'. */ public int getWidth() { return this._width; - } //-- int getWidth() + } //-- int getWidth() /** * Returns the value of field 'wrapAlignment'. - * + * * @return boolean * @return the value of field 'wrapAlignment'. */ public boolean getWrapAlignment() { return this._wrapAlignment; - } //-- boolean getWrapAlignment() + } //-- boolean getWrapAlignment() /** * Returns the value of field 'xpos'. - * + * * @return int * @return the value of field 'xpos'. */ public int getXpos() { return this._xpos; - } //-- int getXpos() + } //-- int getXpos() /** * Returns the value of field 'ypos'. - * + * * @return int * @return the value of field 'ypos'. */ public int getYpos() { return this._ypos; - } //-- int getYpos() + } //-- int getYpos() /** * Method hasConsThreshold - * - * - * + * + * + * * @return boolean */ public boolean hasConsThreshold() { return this._has_consThreshold; - } //-- boolean hasConsThreshold() + } //-- boolean hasConsThreshold() /** * Method hasConservationSelected - * - * - * + * + * + * * @return boolean */ public boolean hasConservationSelected() { return this._has_conservationSelected; - } //-- boolean hasConservationSelected() + } //-- boolean hasConservationSelected() /** * Method hasFontSize - * - * - * + * + * + * * @return boolean */ public boolean hasFontSize() { return this._has_fontSize; - } //-- boolean hasFontSize() + } //-- boolean hasFontSize() /** * Method hasFontStyle - * - * - * + * + * + * * @return boolean */ public boolean hasFontStyle() { return this._has_fontStyle; - } //-- boolean hasFontStyle() + } //-- boolean hasFontStyle() /** * Method hasHeight - * - * - * + * + * + * * @return boolean */ public boolean hasHeight() { return this._has_height; - } //-- boolean hasHeight() + } //-- boolean hasHeight() /** * Method hasPidSelected - * - * - * + * + * + * * @return boolean */ public boolean hasPidSelected() { return this._has_pidSelected; - } //-- boolean hasPidSelected() + } //-- boolean hasPidSelected() /** * Method hasPidThreshold - * - * - * + * + * + * * @return boolean */ public boolean hasPidThreshold() { return this._has_pidThreshold; - } //-- boolean hasPidThreshold() + } //-- boolean hasPidThreshold() /** * Method hasRenderGaps - * - * - * + * + * + * * @return boolean */ public boolean hasRenderGaps() { return this._has_renderGaps; - } //-- boolean hasRenderGaps() + } //-- boolean hasRenderGaps() /** * Method hasShowAnnotation - * - * - * + * + * + * * @return boolean */ public boolean hasShowAnnotation() { return this._has_showAnnotation; - } //-- boolean hasShowAnnotation() + } //-- boolean hasShowAnnotation() /** * Method hasShowBoxes - * - * - * + * + * + * * @return boolean */ public boolean hasShowBoxes() { return this._has_showBoxes; - } //-- boolean hasShowBoxes() + } //-- boolean hasShowBoxes() /** * Method hasShowColourText - * - * - * + * + * + * * @return boolean */ public boolean hasShowColourText() { return this._has_showColourText; - } //-- boolean hasShowColourText() + } //-- boolean hasShowColourText() /** * Method hasShowConservation - * - * - * + * + * + * * @return boolean */ public boolean hasShowConservation() { return this._has_showConservation; - } //-- boolean hasShowConservation() + } //-- boolean hasShowConservation() /** * Method hasShowFullId - * - * - * + * + * + * * @return boolean */ public boolean hasShowFullId() { return this._has_showFullId; - } //-- boolean hasShowFullId() + } //-- boolean hasShowFullId() /** * Method hasShowIdentity - * - * - * + * + * + * * @return boolean */ public boolean hasShowIdentity() { return this._has_showIdentity; - } //-- boolean hasShowIdentity() + } //-- boolean hasShowIdentity() /** * Method hasShowQuality - * - * - * + * + * + * * @return boolean */ public boolean hasShowQuality() { return this._has_showQuality; - } //-- boolean hasShowQuality() + } //-- boolean hasShowQuality() /** * Method hasShowSequenceFeatures - * - * - * + * + * + * * @return boolean */ public boolean hasShowSequenceFeatures() { return this._has_showSequenceFeatures; - } //-- boolean hasShowSequenceFeatures() + } //-- boolean hasShowSequenceFeatures() /** * Method hasShowText - * - * - * + * + * + * * @return boolean */ public boolean hasShowText() { return this._has_showText; - } //-- boolean hasShowText() + } //-- boolean hasShowText() /** * Method hasStartRes - * - * - * + * + * + * * @return boolean */ public boolean hasStartRes() { return this._has_startRes; - } //-- boolean hasStartRes() + } //-- boolean hasStartRes() /** * Method hasStartSeq - * - * - * + * + * + * * @return boolean */ public boolean hasStartSeq() { return this._has_startSeq; - } //-- boolean hasStartSeq() + } //-- boolean hasStartSeq() /** * Method hasWidth - * - * - * + * + * + * * @return boolean */ public boolean hasWidth() { return this._has_width; - } //-- boolean hasWidth() + } //-- boolean hasWidth() /** * Method hasWrapAlignment - * - * - * + * + * + * * @return boolean */ public boolean hasWrapAlignment() { return this._has_wrapAlignment; - } //-- boolean hasWrapAlignment() + } //-- boolean hasWrapAlignment() /** * Method hasXpos - * - * - * + * + * + * * @return boolean */ public boolean hasXpos() { return this._has_xpos; - } //-- boolean hasXpos() + } //-- boolean hasXpos() /** * Method hasYpos - * - * - * + * + * + * * @return boolean */ public boolean hasYpos() { return this._has_ypos; - } //-- boolean hasYpos() + } //-- boolean hasYpos() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -1077,60 +1097,60 @@ public class Viewport implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'bgColour'. - * + * * @param bgColour the value of field 'bgColour'. */ public void setBgColour(java.lang.String bgColour) { this._bgColour = bgColour; - } //-- void setBgColour(java.lang.String) + } //-- void setBgColour(java.lang.String) /** * Sets the value of field 'consThreshold'. - * + * * @param consThreshold the value of field 'consThreshold'. */ public void setConsThreshold(int consThreshold) { this._consThreshold = consThreshold; this._has_consThreshold = true; - } //-- void setConsThreshold(int) + } //-- void setConsThreshold(int) /** * Sets the value of field 'conservationSelected'. - * + * * @param conservationSelected the value of field * 'conservationSelected'. */ @@ -1138,164 +1158,164 @@ public class Viewport implements java.io.Serializable { { this._conservationSelected = conservationSelected; this._has_conservationSelected = true; - } //-- void setConservationSelected(boolean) + } //-- void setConservationSelected(boolean) /** * Sets the value of field 'fontName'. - * + * * @param fontName the value of field 'fontName'. */ public void setFontName(java.lang.String fontName) { this._fontName = fontName; - } //-- void setFontName(java.lang.String) + } //-- void setFontName(java.lang.String) /** * Sets the value of field 'fontSize'. - * + * * @param fontSize the value of field 'fontSize'. */ public void setFontSize(int fontSize) { this._fontSize = fontSize; this._has_fontSize = true; - } //-- void setFontSize(int) + } //-- void setFontSize(int) /** * Sets the value of field 'fontStyle'. - * + * * @param fontStyle the value of field 'fontStyle'. */ public void setFontStyle(int fontStyle) { this._fontStyle = fontStyle; this._has_fontStyle = true; - } //-- void setFontStyle(int) + } //-- void setFontStyle(int) /** * Sets the value of field 'height'. - * + * * @param height the value of field 'height'. */ public void setHeight(int height) { this._height = height; this._has_height = true; - } //-- void setHeight(int) + } //-- void setHeight(int) /** * Sets the value of field 'pidSelected'. - * + * * @param pidSelected the value of field 'pidSelected'. */ public void setPidSelected(boolean pidSelected) { this._pidSelected = pidSelected; this._has_pidSelected = true; - } //-- void setPidSelected(boolean) + } //-- void setPidSelected(boolean) /** * Sets the value of field 'pidThreshold'. - * + * * @param pidThreshold the value of field 'pidThreshold'. */ public void setPidThreshold(int pidThreshold) { this._pidThreshold = pidThreshold; this._has_pidThreshold = true; - } //-- void setPidThreshold(int) + } //-- void setPidThreshold(int) /** * Sets the value of field 'renderGaps'. - * + * * @param renderGaps the value of field 'renderGaps'. */ public void setRenderGaps(boolean renderGaps) { this._renderGaps = renderGaps; this._has_renderGaps = true; - } //-- void setRenderGaps(boolean) + } //-- void setRenderGaps(boolean) /** * Sets the value of field 'showAnnotation'. - * + * * @param showAnnotation the value of field 'showAnnotation'. */ public void setShowAnnotation(boolean showAnnotation) { this._showAnnotation = showAnnotation; this._has_showAnnotation = true; - } //-- void setShowAnnotation(boolean) + } //-- void setShowAnnotation(boolean) /** * Sets the value of field 'showBoxes'. - * + * * @param showBoxes the value of field 'showBoxes'. */ public void setShowBoxes(boolean showBoxes) { this._showBoxes = showBoxes; this._has_showBoxes = true; - } //-- void setShowBoxes(boolean) + } //-- void setShowBoxes(boolean) /** * Sets the value of field 'showColourText'. - * + * * @param showColourText the value of field 'showColourText'. */ public void setShowColourText(boolean showColourText) { this._showColourText = showColourText; this._has_showColourText = true; - } //-- void setShowColourText(boolean) + } //-- void setShowColourText(boolean) /** * Sets the value of field 'showConservation'. - * + * * @param showConservation the value of field 'showConservation' */ public void setShowConservation(boolean showConservation) { this._showConservation = showConservation; this._has_showConservation = true; - } //-- void setShowConservation(boolean) + } //-- void setShowConservation(boolean) /** * Sets the value of field 'showFullId'. - * + * * @param showFullId the value of field 'showFullId'. */ public void setShowFullId(boolean showFullId) { this._showFullId = showFullId; this._has_showFullId = true; - } //-- void setShowFullId(boolean) + } //-- void setShowFullId(boolean) /** * Sets the value of field 'showIdentity'. - * + * * @param showIdentity the value of field 'showIdentity'. */ public void setShowIdentity(boolean showIdentity) { this._showIdentity = showIdentity; this._has_showIdentity = true; - } //-- void setShowIdentity(boolean) + } //-- void setShowIdentity(boolean) /** * Sets the value of field 'showQuality'. - * + * * @param showQuality the value of field 'showQuality'. */ public void setShowQuality(boolean showQuality) { this._showQuality = showQuality; this._has_showQuality = true; - } //-- void setShowQuality(boolean) + } //-- void setShowQuality(boolean) /** * Sets the value of field 'showSequenceFeatures'. - * + * * @param showSequenceFeatures the value of field * 'showSequenceFeatures'. */ @@ -1303,100 +1323,100 @@ public class Viewport implements java.io.Serializable { { this._showSequenceFeatures = showSequenceFeatures; this._has_showSequenceFeatures = true; - } //-- void setShowSequenceFeatures(boolean) + } //-- void setShowSequenceFeatures(boolean) /** * Sets the value of field 'showText'. - * + * * @param showText the value of field 'showText'. */ public void setShowText(boolean showText) { this._showText = showText; this._has_showText = true; - } //-- void setShowText(boolean) + } //-- void setShowText(boolean) /** * Sets the value of field 'startRes'. - * + * * @param startRes the value of field 'startRes'. */ public void setStartRes(int startRes) { this._startRes = startRes; this._has_startRes = true; - } //-- void setStartRes(int) + } //-- void setStartRes(int) /** * Sets the value of field 'startSeq'. - * + * * @param startSeq the value of field 'startSeq'. */ public void setStartSeq(int startSeq) { this._startSeq = startSeq; this._has_startSeq = true; - } //-- void setStartSeq(int) + } //-- void setStartSeq(int) /** * Sets the value of field 'title'. - * + * * @param title the value of field 'title'. */ public void setTitle(java.lang.String title) { this._title = title; - } //-- void setTitle(java.lang.String) + } //-- void setTitle(java.lang.String) /** * Sets the value of field 'width'. - * + * * @param width the value of field 'width'. */ public void setWidth(int width) { this._width = width; this._has_width = true; - } //-- void setWidth(int) + } //-- void setWidth(int) /** * Sets the value of field 'wrapAlignment'. - * + * * @param wrapAlignment the value of field 'wrapAlignment'. */ public void setWrapAlignment(boolean wrapAlignment) { this._wrapAlignment = wrapAlignment; this._has_wrapAlignment = true; - } //-- void setWrapAlignment(boolean) + } //-- void setWrapAlignment(boolean) /** * Sets the value of field 'xpos'. - * + * * @param xpos the value of field 'xpos'. */ public void setXpos(int xpos) { this._xpos = xpos; this._has_xpos = true; - } //-- void setXpos(int) + } //-- void setXpos(int) /** * Sets the value of field 'ypos'. - * + * * @param ypos the value of field 'ypos'. */ public void setYpos(int ypos) { this._ypos = ypos; this._has_ypos = true; - } //-- void setYpos(int) + } //-- void setYpos(int) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -1404,17 +1424,17 @@ public class Viewport implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() } diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 9deb7e2..804414a 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import jalview.analysis.*; diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 7b558c3..337d879 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; public class AlignmentAnnotation diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index b46a1a7..e48ff36 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import java.util.*; diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java index 445671d..3e6fd9f 100755 --- a/src/jalview/datamodel/AlignmentOrder.java +++ b/src/jalview/datamodel/AlignmentOrder.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import java.util.*; diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java index 16ede50..b99ce9f 100755 --- a/src/jalview/datamodel/Annotation.java +++ b/src/jalview/datamodel/Annotation.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import java.awt.*; diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java index 6fb3be2..cefbc22 100755 --- a/src/jalview/datamodel/BinaryNode.java +++ b/src/jalview/datamodel/BinaryNode.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; public class BinaryNode diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java index dffa1a6..63c8d86 100755 --- a/src/jalview/datamodel/BinarySequence.java +++ b/src/jalview/datamodel/BinarySequence.java @@ -1,20 +1,22 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import jalview.io.*; diff --git a/src/jalview/datamodel/HistoryItem.java b/src/jalview/datamodel/HistoryItem.java index 3a5b180..bb18b66 100755 --- a/src/jalview/datamodel/HistoryItem.java +++ b/src/jalview/datamodel/HistoryItem.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import java.util.*; diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index ab35c38..d7f2b9f 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import jalview.analysis.*; diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index a197dfd..a2856fa 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import java.awt.*; diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 63fefdd..d6ea5dd 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import jalview.schemes.*; diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 36afd4b..9c2ab48 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import jalview.jbgui.*; diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java index 5e16c57..74776ea 100755 --- a/src/jalview/datamodel/SequenceNode.java +++ b/src/jalview/datamodel/SequenceNode.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import java.awt.*; diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java index 093c45a..5da4d64 100755 --- a/src/jalview/datamodel/SequencePoint.java +++ b/src/jalview/datamodel/SequencePoint.java @@ -1,20 +1,21 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.datamodel; import java.util.*; diff --git a/src/jalview/datamodel/SuperGroup.java b/src/jalview/datamodel/SuperGroup.java index 4e2ac1c..cd86ef6 100755 --- a/src/jalview/datamodel/SuperGroup.java +++ b/src/jalview/datamodel/SuperGroup.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.datamodel; import jalview.schemes.*; diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 4d97f49..8cb12d1 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,13 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ - - - +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.gui; @@ -991,7 +999,7 @@ public class AlignFrame extends GAlignFrame public void sortGroupMenuItem_actionPerformed(ActionEvent e) { addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT)); - AlignmentSorter.sortByGroup(viewport.getAlignment()); + // AlignmentSorter.sortByGroup(viewport.getAlignment()); AlignmentSorter.sortGroups(viewport.getAlignment()); alignPanel.repaint(); } diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index fe03a31..1f5ec79 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import java.awt.*; diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 9895753..7a8a811 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.jbgui.GAlignmentPanel; diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 3f7b5ad..f2603ea 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,4 +1,23 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import javax.swing.*; diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index b8d35dc..41bbb43 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.datamodel.*; diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java index 7d1e474..5761184 100755 --- a/src/jalview/gui/ColumnSelection.java +++ b/src/jalview/gui/ColumnSelection.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import java.util.*; diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index 5f615f4..262fc41 100755 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.gui; diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index b6fd73e..fca0acc 100755 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,11 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ - +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.gui; diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 837304e..1dd434d 100755 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.datamodel.*; diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index ef28ebe..d20cb65 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.jbgui.GFinder; diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java index db84487..d781d72 100755 --- a/src/jalview/gui/FontChooser.java +++ b/src/jalview/gui/FontChooser.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.jbgui.GFontChooser; diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index 4f5288d..c523060 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import java.awt.*; diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 12bf8d4..4236cf8 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import java.awt.*; diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java index 6872136..ead38dc 100755 --- a/src/jalview/gui/IdwidthAdjuster.java +++ b/src/jalview/gui/IdwidthAdjuster.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import javax.swing.*; diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index fa8e50b..89a7bfc 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import java.io.*; @@ -8,6 +27,7 @@ import jalview.binding.*; import jalview.schemes.*; import javax.swing.JInternalFrame; import java.net.URL; +import jalview.io.SequenceFeatureFetcher; public class Jalview2XML @@ -505,6 +525,8 @@ public class Jalview2XML view.getFontStyle(), view.getFontSize())); af.alignPanel.fontChanged(); + + af.sequenceFeatures_actionPerformed(null); af.viewport.setRenderGaps( view.getRenderGaps() ); af.viewport.setWrapAlignment( view.getWrapAlignment() ); @@ -546,6 +568,11 @@ public class Jalview2XML af.changeColour(af.viewport.getGlobalColourScheme()); af.viewport.setColourAppliesToAllGroups(true); + System.out.println(view.getShowSequenceFeatures()); + if( view.getShowSequenceFeatures() ); + { + SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, af.alignPanel); + } //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE if(object.getVamsasModel().getTreeCount()>0) diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index a0d8151..a55af89 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import javax.swing.*; diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index d0b3bbc..8f3ff73 100755 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.datamodel.*; diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java index c60e29a..12545af 100755 --- a/src/jalview/gui/PaintRefresher.java +++ b/src/jalview/gui/PaintRefresher.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import java.awt.*; import java.util.*; diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java index 76f4eb5..2825467 100755 --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.datamodel.*; diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index d85fabc..7133e44 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.datamodel.*; diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index f305bd4..4708ced 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.jbgui.*; diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index 5d266f8..e4ef46e 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.jbgui.*; diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java index 9dc5754..0d5025e 100755 --- a/src/jalview/gui/RotatableCanvas.java +++ b/src/jalview/gui/RotatableCanvas.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.math.*; diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java index 2ec4570..de0a7b1 100755 --- a/src/jalview/gui/ScalePanel.java +++ b/src/jalview/gui/ScalePanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.datamodel.*; diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index b2e9d3e..d40f971 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import java.awt.*; diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index b48861a..44cf4d4 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import java.awt.*; diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 8cab563..2c98754 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.datamodel.*; diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java index 5a87102..97c5e10 100755 --- a/src/jalview/gui/SliderPanel.java +++ b/src/jalview/gui/SliderPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.jbgui.*; diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java index faaf62e..794bbb8 100755 --- a/src/jalview/gui/SplashScreen.java +++ b/src/jalview/gui/SplashScreen.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import javax.swing.*; diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index f9cb39c..5ebf323 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index fd688e6..a574795 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.datamodel.*; diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 5fdcdf8..f0cf6c1 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import jalview.jbgui.GUserDefinedColours; diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java index 82350d1..9e980c5 100755 --- a/src/jalview/gui/WebserviceInfo.java +++ b/src/jalview/gui/WebserviceInfo.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.gui; import java.awt.*; diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 77002cf..0dfef6a 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import jalview.datamodel.*; diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java index 84d8a9d..7961810 100755 --- a/src/jalview/io/BLCFile.java +++ b/src/jalview/io/BLCFile.java @@ -1,20 +1,22 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import jalview.datamodel.*; diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java index 3594afa..9b56526 100755 --- a/src/jalview/io/ClustalFile.java +++ b/src/jalview/io/ClustalFile.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import jalview.datamodel.*; diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java index db34357..3c6e5f9 100755 --- a/src/jalview/io/EBIFetchClient.java +++ b/src/jalview/io/EBIFetchClient.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import org.apache.axis.client.*; diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java index cd287ff..7910340 100755 --- a/src/jalview/io/FastaFile.java +++ b/src/jalview/io/FastaFile.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import jalview.datamodel.*; diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 5f2e856..ea86ae0 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import java.io.*; diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 3e5e250..0382cee 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import jalview.datamodel.*; diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java index 50f7471..290dee7 100755 --- a/src/jalview/io/HTMLOutput.java +++ b/src/jalview/io/HTMLOutput.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import jalview.gui.*; diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index fa4aba6..f1cf1e0 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.io; diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index b2226db..38addf7 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -1,8 +1,28 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + /** * PredFile.java * JalviewX / Vamsas Project * JPred.seq.concise reader */ + package jalview.io; import jalview.datamodel.*; diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java index eca6e43..5a29ba7 100755 --- a/src/jalview/io/JalviewFileChooser.java +++ b/src/jalview/io/JalviewFileChooser.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + /*/////////////////////////////////////////////////////////////////// // This file was taken from java forum diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java index f19e5ea..d6c6d4b 100755 --- a/src/jalview/io/JalviewFileFilter.java +++ b/src/jalview/io/JalviewFileFilter.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import javax.swing.filechooser.*; diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java index 3c96a28..4df6576 100755 --- a/src/jalview/io/JalviewFileView.java +++ b/src/jalview/io/JalviewFileView.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import javax.swing.filechooser.FileView; diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java index 63827a1..104b9d7 100755 --- a/src/jalview/io/MSFfile.java +++ b/src/jalview/io/MSFfile.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import jalview.datamodel.*; diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index 85ab084..a372ed3 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -1,6 +1,26 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + // NewickFile.java // Tree I/O // http://evolution.genetics.washington.edu/phylip/newick_doc.html + package jalview.io; import java.io.*; diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java index be60a43..410628f 100755 --- a/src/jalview/io/PIRFile.java +++ b/src/jalview/io/PIRFile.java @@ -1,20 +1,22 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import jalview.datamodel.*; diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java index 3a02041..d0ffbc9 100755 --- a/src/jalview/io/PfamFile.java +++ b/src/jalview/io/PfamFile.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import jalview.datamodel.*; diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java index 387596d..f5f709e 100755 --- a/src/jalview/io/PileUpfile.java +++ b/src/jalview/io/PileUpfile.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; /** diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java index 8cfa6b8..b8300a0 100755 --- a/src/jalview/io/SequenceFeatureFetcher.java +++ b/src/jalview/io/SequenceFeatureFetcher.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import java.io.*; diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java index f8d74bf..fd82c9e 100755 --- a/src/jalview/io/WSWUBlastClient.java +++ b/src/jalview/io/WSWUBlastClient.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.io; import org.apache.axis.client.*; diff --git a/src/jalview/jbappletgui/GAlignFrame.java b/src/jalview/jbappletgui/GAlignFrame.java index 9bc7525..58c8029 100755 --- a/src/jalview/jbappletgui/GAlignFrame.java +++ b/src/jalview/jbappletgui/GAlignFrame.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.jbappletgui; diff --git a/src/jalview/jbappletgui/GAlignmentPanel.java b/src/jalview/jbappletgui/GAlignmentPanel.java index 4825e29..272e8df 100755 --- a/src/jalview/jbappletgui/GAlignmentPanel.java +++ b/src/jalview/jbappletgui/GAlignmentPanel.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.jbappletgui; diff --git a/src/jalview/jbappletgui/GCutAndPasteTransfer.java b/src/jalview/jbappletgui/GCutAndPasteTransfer.java index ca5b6d8..33fe5a6 100755 --- a/src/jalview/jbappletgui/GCutAndPasteTransfer.java +++ b/src/jalview/jbappletgui/GCutAndPasteTransfer.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.jbappletgui; diff --git a/src/jalview/jbappletgui/GFinder.java b/src/jalview/jbappletgui/GFinder.java index 5a1afbe..283b28d 100755 --- a/src/jalview/jbappletgui/GFinder.java +++ b/src/jalview/jbappletgui/GFinder.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbappletgui; import java.awt.*; diff --git a/src/jalview/jbappletgui/GFontChooser.java b/src/jalview/jbappletgui/GFontChooser.java index d83ed0d..1c087c5 100755 --- a/src/jalview/jbappletgui/GFontChooser.java +++ b/src/jalview/jbappletgui/GFontChooser.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbappletgui; import java.awt.*; diff --git a/src/jalview/jbappletgui/GPCAPanel.java b/src/jalview/jbappletgui/GPCAPanel.java index ad8a02e..b13b563 100755 --- a/src/jalview/jbappletgui/GPCAPanel.java +++ b/src/jalview/jbappletgui/GPCAPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbappletgui; import java.awt.*; diff --git a/src/jalview/jbappletgui/GPairwiseAlignPanel.java b/src/jalview/jbappletgui/GPairwiseAlignPanel.java index ecf3c8d..54bb555 100755 --- a/src/jalview/jbappletgui/GPairwiseAlignPanel.java +++ b/src/jalview/jbappletgui/GPairwiseAlignPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbappletgui; import java.awt.*; diff --git a/src/jalview/jbappletgui/GSliderPanel.java b/src/jalview/jbappletgui/GSliderPanel.java index 8f7613a..d8120b4 100755 --- a/src/jalview/jbappletgui/GSliderPanel.java +++ b/src/jalview/jbappletgui/GSliderPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbappletgui; import java.awt.*; diff --git a/src/jalview/jbappletgui/GTreePanel.java b/src/jalview/jbappletgui/GTreePanel.java index f0e28e1..a663402 100755 --- a/src/jalview/jbappletgui/GTreePanel.java +++ b/src/jalview/jbappletgui/GTreePanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbappletgui; import java.awt.*; diff --git a/src/jalview/jbappletgui/GUserDefinedColours.java b/src/jalview/jbappletgui/GUserDefinedColours.java index 47170b2..0acc0b1 100755 --- a/src/jalview/jbappletgui/GUserDefinedColours.java +++ b/src/jalview/jbappletgui/GUserDefinedColours.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbappletgui; import java.awt.*; diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 23c78f3..00b4bc9 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.jbgui; diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java index d9e576a..fc6fc1e 100755 --- a/src/jalview/jbgui/GAlignmentPanel.java +++ b/src/jalview/jbgui/GAlignmentPanel.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.jbgui; diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java index e9a0164..7b0c621 100755 --- a/src/jalview/jbgui/GCutAndPasteTransfer.java +++ b/src/jalview/jbgui/GCutAndPasteTransfer.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.jbgui; diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java index 2642d9c..1dc49b7 100755 --- a/src/jalview/jbgui/GDesktop.java +++ b/src/jalview/jbgui/GDesktop.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.jbgui; diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java index 3720d67..b7cd2e8 100755 --- a/src/jalview/jbgui/GFinder.java +++ b/src/jalview/jbgui/GFinder.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbgui; import javax.swing.*; diff --git a/src/jalview/jbgui/GFontChooser.java b/src/jalview/jbgui/GFontChooser.java index ab0b080..5966af5 100755 --- a/src/jalview/jbgui/GFontChooser.java +++ b/src/jalview/jbgui/GFontChooser.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbgui; import javax.swing.*; diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java index 717c817..84e84c4 100755 --- a/src/jalview/jbgui/GPCAPanel.java +++ b/src/jalview/jbgui/GPCAPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbgui; import java.awt.*; diff --git a/src/jalview/jbgui/GPairwiseAlignPanel.java b/src/jalview/jbgui/GPairwiseAlignPanel.java index 77c0d79..e8167cf 100755 --- a/src/jalview/jbgui/GPairwiseAlignPanel.java +++ b/src/jalview/jbgui/GPairwiseAlignPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbgui; import javax.swing.*; diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index f9b7ba9..1ead51c 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbgui; import javax.swing.*; diff --git a/src/jalview/jbgui/GSliderPanel.java b/src/jalview/jbgui/GSliderPanel.java index 77911b4..17fdb34 100755 --- a/src/jalview/jbgui/GSliderPanel.java +++ b/src/jalview/jbgui/GSliderPanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbgui; import java.awt.*; diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java index 7fd33f0..93bb850 100755 --- a/src/jalview/jbgui/GTreePanel.java +++ b/src/jalview/jbgui/GTreePanel.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbgui; import java.awt.*; diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java index dc4f291..4d62593 100755 --- a/src/jalview/jbgui/GUserDefinedColours.java +++ b/src/jalview/jbgui/GUserDefinedColours.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbgui; import javax.swing.*; diff --git a/src/jalview/jbgui/GWebserviceInfo.java b/src/jalview/jbgui/GWebserviceInfo.java index 71988b3..4d3aab6 100755 --- a/src/jalview/jbgui/GWebserviceInfo.java +++ b/src/jalview/jbgui/GWebserviceInfo.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.jbgui; import java.awt.*; diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java index 0f45978..3b93d6d 100755 --- a/src/jalview/math/Matrix.java +++ b/src/jalview/math/Matrix.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.math; import jalview.util.*; diff --git a/src/jalview/math/RotatableMatrix.java b/src/jalview/math/RotatableMatrix.java index dfe09f1..d9f4bd5 100755 --- a/src/jalview/math/RotatableMatrix.java +++ b/src/jalview/math/RotatableMatrix.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.math; diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java index 566d7ed..40243f2 100755 --- a/src/jalview/schemes/Blosum62ColourScheme.java +++ b/src/jalview/schemes/Blosum62ColourScheme.java @@ -1,20 +1,21 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.schemes; diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java index 34faf70..8b0305d 100755 --- a/src/jalview/schemes/BuriedColourScheme.java +++ b/src/jalview/schemes/BuriedColourScheme.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.schemes; import java.awt.*; diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java index fe1289e..bbca4de 100755 --- a/src/jalview/schemes/ClustalxColourScheme.java +++ b/src/jalview/schemes/ClustalxColourScheme.java @@ -1,20 +1,21 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.schemes; diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java index 495947a..250cae5 100755 --- a/src/jalview/schemes/ColourSchemeI.java +++ b/src/jalview/schemes/ColourSchemeI.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.schemes; import java.awt.*; diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 8317bd7..a981549 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.schemes; public class ColourSchemeProperty diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java index 17cb789..27c5906 100755 --- a/src/jalview/schemes/Consensus.java +++ b/src/jalview/schemes/Consensus.java @@ -1,20 +1,21 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.schemes; diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java index 6394124..8c3f694 100755 --- a/src/jalview/schemes/ConservationColourScheme.java +++ b/src/jalview/schemes/ConservationColourScheme.java @@ -1,20 +1,21 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.schemes; import java.awt.*; diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java index 6c2f744..35e1a26 100755 --- a/src/jalview/schemes/HelixColourScheme.java +++ b/src/jalview/schemes/HelixColourScheme.java @@ -1,20 +1,21 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.schemes; diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java index 575d1b2..e1eef48 100755 --- a/src/jalview/schemes/HydrophobicColourScheme.java +++ b/src/jalview/schemes/HydrophobicColourScheme.java @@ -1,20 +1,21 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.schemes; diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java index 5c65894..0f2101e 100755 --- a/src/jalview/schemes/NucleotideColourScheme.java +++ b/src/jalview/schemes/NucleotideColourScheme.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.schemes; import java.awt.*; diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java index eadf09b..34c47ed 100755 --- a/src/jalview/schemes/PIDColourScheme.java +++ b/src/jalview/schemes/PIDColourScheme.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.schemes; import jalview.datamodel.*; diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 3bd9bca..e90e6cc 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.schemes; import java.util.*; diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index f7c13ef..002917b 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -1,5 +1,6 @@ - -/* Copyright (C) 1998 Michele Clamp +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -13,8 +14,9 @@ * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software -* Foundation, Inc, 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ + package jalview.schemes; import java.awt.Color; diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java index 220aecc..b6dc45b 100755 --- a/src/jalview/schemes/ScoreColourScheme.java +++ b/src/jalview/schemes/ScoreColourScheme.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.schemes; import java.awt.*; diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java index 1e54a74..466ae4f 100755 --- a/src/jalview/schemes/StrandColourScheme.java +++ b/src/jalview/schemes/StrandColourScheme.java @@ -1,21 +1,21 @@ - -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.schemes; diff --git a/src/jalview/schemes/TaylorColourScheme.java b/src/jalview/schemes/TaylorColourScheme.java index 2658673..490425e 100755 --- a/src/jalview/schemes/TaylorColourScheme.java +++ b/src/jalview/schemes/TaylorColourScheme.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.schemes; public class TaylorColourScheme extends ResidueColourScheme { diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java index 6d0f7aa..2964bae 100755 --- a/src/jalview/schemes/TurnColourScheme.java +++ b/src/jalview/schemes/TurnColourScheme.java @@ -1,20 +1,21 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.schemes; diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java index e6f6c9f..b4decde 100755 --- a/src/jalview/schemes/UserColourScheme.java +++ b/src/jalview/schemes/UserColourScheme.java @@ -1,20 +1,21 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.schemes; diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java index 7cb2327..e042acb 100755 --- a/src/jalview/schemes/ZappoColourScheme.java +++ b/src/jalview/schemes/ZappoColourScheme.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.schemes; public class ZappoColourScheme extends ResidueColourScheme { diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java index 5404c77..aef74d5 100755 --- a/src/jalview/util/BrowserLauncher.java +++ b/src/jalview/util/BrowserLauncher.java @@ -1,10 +1,21 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.util; diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java index 181dea5..320855a 100755 --- a/src/jalview/util/Comparison.java +++ b/src/jalview/util/Comparison.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.util; import jalview.datamodel.*; diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java index 826adf6..798dc8f 100755 --- a/src/jalview/util/Format.java +++ b/src/jalview/util/Format.java @@ -26,6 +26,7 @@ * @author Cay Horstmann */ + package jalview.util; import java.io.*; diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java index f81056a..3624144 100755 --- a/src/jalview/util/QuickSort.java +++ b/src/jalview/util/QuickSort.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.util; diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 8d3ae35..674743e 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.ws; import org.apache.axis.client.*; diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java index 91f0786..32f5c43 100755 --- a/src/jalview/ws/MsaWSClient.java +++ b/src/jalview/ws/MsaWSClient.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.ws; import org.apache.axis.client.*; diff --git a/src/jalview/ws/MsaWServices.java b/src/jalview/ws/MsaWServices.java index 69b5e23..f881bd5 100755 --- a/src/jalview/ws/MsaWServices.java +++ b/src/jalview/ws/MsaWServices.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.ws; import java.util.Hashtable; /** diff --git a/src/jalview/ws/WSClient.java b/src/jalview/ws/WSClient.java index 80414ef..1d03eab 100755 --- a/src/jalview/ws/WSClient.java +++ b/src/jalview/ws/WSClient.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.ws; import jalview.gui.WebserviceInfo; diff --git a/src/jalview/ws/WSClientI.java b/src/jalview/ws/WSClientI.java index 2474078..7bd4ab8 100755 --- a/src/jalview/ws/WSClientI.java +++ b/src/jalview/ws/WSClientI.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package jalview.ws; public interface WSClientI diff --git a/src/vamsas/IMsaWS.java b/src/vamsas/IMsaWS.java index 9555b91..ed31920 100755 --- a/src/vamsas/IMsaWS.java +++ b/src/vamsas/IMsaWS.java @@ -1,8 +1,21 @@ -/* MsaWS.java - * The basic Multiple Sequence Alignment interface - * J.B. Procter Feb 2004 - * @header - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package vamsas; diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java index 18fa20c..177d373 100755 --- a/src/vamsas/objects/simple/Alignment.java +++ b/src/vamsas/objects/simple/Alignment.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class Alignment extends vamsas.objects.simple.Object implements java.io.Serializable { @@ -27,7 +46,7 @@ public class Alignment extends vamsas.objects.simple.Object implements java.io /** * Gets the gapchar value for this Alignment. - * + * * @return gapchar */ public java.lang.String getGapchar() { @@ -37,7 +56,7 @@ public class Alignment extends vamsas.objects.simple.Object implements java.io /** * Sets the gapchar value for this Alignment. - * + * * @param gapchar */ public void setGapchar(java.lang.String gapchar) { @@ -47,7 +66,7 @@ public class Alignment extends vamsas.objects.simple.Object implements java.io /** * Gets the method value for this Alignment. - * + * * @return method */ public java.lang.String[] getMethod() { @@ -57,7 +76,7 @@ public class Alignment extends vamsas.objects.simple.Object implements java.io /** * Sets the method value for this Alignment. - * + * * @param method */ public void setMethod(java.lang.String[] method) { @@ -67,7 +86,7 @@ public class Alignment extends vamsas.objects.simple.Object implements java.io /** * Gets the seqs value for this Alignment. - * + * * @return seqs */ public vamsas.objects.simple.SequenceSet getSeqs() { @@ -77,7 +96,7 @@ public class Alignment extends vamsas.objects.simple.Object implements java.io /** * Sets the seqs value for this Alignment. - * + * * @param seqs */ public void setSeqs(vamsas.objects.simple.SequenceSet seqs) { @@ -95,14 +114,14 @@ public class Alignment extends vamsas.objects.simple.Object implements java.io } __equalsCalc = obj; boolean _equals; - _equals = super.equals(obj) && - ((this.gapchar==null && other.getGapchar()==null) || + _equals = super.equals(obj) && + ((this.gapchar==null && other.getGapchar()==null) || (this.gapchar!=null && this.gapchar.equals(other.getGapchar()))) && - ((this.method==null && other.getMethod()==null) || + ((this.method==null && other.getMethod()==null) || (this.method!=null && java.util.Arrays.equals(this.method, other.getMethod()))) && - ((this.seqs==null && other.getSeqs()==null) || + ((this.seqs==null && other.getSeqs()==null) || (this.seqs!=null && this.seqs.equals(other.getSeqs()))); __equalsCalc = null; diff --git a/src/vamsas/objects/simple/Alignment_Helper.java b/src/vamsas/objects/simple/Alignment_Helper.java index 5a54fe0..57cd7ca 100755 --- a/src/vamsas/objects/simple/Alignment_Helper.java +++ b/src/vamsas/objects/simple/Alignment_Helper.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class Alignment_Helper { @@ -42,10 +61,10 @@ public class Alignment_Helper { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -54,10 +73,10 @@ public class Alignment_Helper { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/vamsas/objects/simple/MsaResult.java b/src/vamsas/objects/simple/MsaResult.java index 97000e4..e4af81e 100755 --- a/src/vamsas/objects/simple/MsaResult.java +++ b/src/vamsas/objects/simple/MsaResult.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class MsaResult extends vamsas.objects.simple.Result implements java.io.Serializable { @@ -21,7 +40,7 @@ public class MsaResult extends vamsas.objects.simple.Result implements java.io /** * Gets the msa value for this MsaResult. - * + * * @return msa */ public vamsas.objects.simple.Alignment getMsa() { @@ -31,7 +50,7 @@ public class MsaResult extends vamsas.objects.simple.Result implements java.io /** * Sets the msa value for this MsaResult. - * + * * @param msa */ public void setMsa(vamsas.objects.simple.Alignment msa) { @@ -49,8 +68,8 @@ public class MsaResult extends vamsas.objects.simple.Result implements java.io } __equalsCalc = obj; boolean _equals; - _equals = super.equals(obj) && - ((this.msa==null && other.getMsa()==null) || + _equals = super.equals(obj) && + ((this.msa==null && other.getMsa()==null) || (this.msa!=null && this.msa.equals(other.getMsa()))); __equalsCalc = null; diff --git a/src/vamsas/objects/simple/MsaResult_Helper.java b/src/vamsas/objects/simple/MsaResult_Helper.java index c950f18..ff8aefc 100755 --- a/src/vamsas/objects/simple/MsaResult_Helper.java +++ b/src/vamsas/objects/simple/MsaResult_Helper.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class MsaResult_Helper { @@ -32,10 +51,10 @@ public class MsaResult_Helper { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -44,10 +63,10 @@ public class MsaResult_Helper { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/vamsas/objects/simple/Object.java b/src/vamsas/objects/simple/Object.java index 4bf69bd..ea22e9e 100755 --- a/src/vamsas/objects/simple/Object.java +++ b/src/vamsas/objects/simple/Object.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public abstract class Object implements java.io.Serializable { diff --git a/src/vamsas/objects/simple/Object_Helper.java b/src/vamsas/objects/simple/Object_Helper.java index a1b944c..e6012f4 100755 --- a/src/vamsas/objects/simple/Object_Helper.java +++ b/src/vamsas/objects/simple/Object_Helper.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class Object_Helper { @@ -27,10 +46,10 @@ public class Object_Helper { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -39,10 +58,10 @@ public class Object_Helper { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/vamsas/objects/simple/Result.java b/src/vamsas/objects/simple/Result.java index b349019..1444911 100755 --- a/src/vamsas/objects/simple/Result.java +++ b/src/vamsas/objects/simple/Result.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class Result implements java.io.Serializable { @@ -51,7 +70,7 @@ public class Result implements java.io.Serializable { /** * Gets the broken value for this Result. - * + * * @return broken */ public boolean isBroken() { @@ -61,7 +80,7 @@ public class Result implements java.io.Serializable { /** * Sets the broken value for this Result. - * + * * @param broken */ public void setBroken(boolean broken) { @@ -71,7 +90,7 @@ public class Result implements java.io.Serializable { /** * Gets the failed value for this Result. - * + * * @return failed */ public boolean isFailed() { @@ -81,7 +100,7 @@ public class Result implements java.io.Serializable { /** * Sets the failed value for this Result. - * + * * @param failed */ public void setFailed(boolean failed) { @@ -91,7 +110,7 @@ public class Result implements java.io.Serializable { /** * Gets the finished value for this Result. - * + * * @return finished */ public boolean isFinished() { @@ -101,7 +120,7 @@ public class Result implements java.io.Serializable { /** * Sets the finished value for this Result. - * + * * @param finished */ public void setFinished(boolean finished) { @@ -111,7 +130,7 @@ public class Result implements java.io.Serializable { /** * Gets the invalid value for this Result. - * + * * @return invalid */ public boolean isInvalid() { @@ -121,7 +140,7 @@ public class Result implements java.io.Serializable { /** * Sets the invalid value for this Result. - * + * * @param invalid */ public void setInvalid(boolean invalid) { @@ -131,7 +150,7 @@ public class Result implements java.io.Serializable { /** * Gets the jobFailed value for this Result. - * + * * @return jobFailed */ public boolean isJobFailed() { @@ -141,7 +160,7 @@ public class Result implements java.io.Serializable { /** * Sets the jobFailed value for this Result. - * + * * @param jobFailed */ public void setJobFailed(boolean jobFailed) { @@ -151,7 +170,7 @@ public class Result implements java.io.Serializable { /** * Gets the queued value for this Result. - * + * * @return queued */ public boolean isQueued() { @@ -161,7 +180,7 @@ public class Result implements java.io.Serializable { /** * Sets the queued value for this Result. - * + * * @param queued */ public void setQueued(boolean queued) { @@ -171,7 +190,7 @@ public class Result implements java.io.Serializable { /** * Gets the running value for this Result. - * + * * @return running */ public boolean isRunning() { @@ -181,7 +200,7 @@ public class Result implements java.io.Serializable { /** * Sets the running value for this Result. - * + * * @param running */ public void setRunning(boolean running) { @@ -191,7 +210,7 @@ public class Result implements java.io.Serializable { /** * Gets the serverError value for this Result. - * + * * @return serverError */ public boolean isServerError() { @@ -201,7 +220,7 @@ public class Result implements java.io.Serializable { /** * Sets the serverError value for this Result. - * + * * @param serverError */ public void setServerError(boolean serverError) { @@ -211,7 +230,7 @@ public class Result implements java.io.Serializable { /** * Gets the state value for this Result. - * + * * @return state */ public int getState() { @@ -221,7 +240,7 @@ public class Result implements java.io.Serializable { /** * Sets the state value for this Result. - * + * * @param state */ public void setState(int state) { @@ -231,7 +250,7 @@ public class Result implements java.io.Serializable { /** * Gets the status value for this Result. - * + * * @return status */ public java.lang.String getStatus() { @@ -241,7 +260,7 @@ public class Result implements java.io.Serializable { /** * Sets the status value for this Result. - * + * * @param status */ public void setStatus(java.lang.String status) { @@ -251,7 +270,7 @@ public class Result implements java.io.Serializable { /** * Gets the suspended value for this Result. - * + * * @return suspended */ public boolean isSuspended() { @@ -261,7 +280,7 @@ public class Result implements java.io.Serializable { /** * Sets the suspended value for this Result. - * + * * @param suspended */ public void setSuspended(boolean suspended) { @@ -279,7 +298,7 @@ public class Result implements java.io.Serializable { } __equalsCalc = obj; boolean _equals; - _equals = true && + _equals = true && this.broken == other.isBroken() && this.failed == other.isFailed() && this.finished == other.isFinished() && @@ -289,7 +308,7 @@ public class Result implements java.io.Serializable { this.running == other.isRunning() && this.serverError == other.isServerError() && this.state == other.getState() && - ((this.status==null && other.getStatus()==null) || + ((this.status==null && other.getStatus()==null) || (this.status!=null && this.status.equals(other.getStatus()))) && this.suspended == other.isSuspended(); diff --git a/src/vamsas/objects/simple/Result_Helper.java b/src/vamsas/objects/simple/Result_Helper.java index 14ed2b5..f61a0c9 100755 --- a/src/vamsas/objects/simple/Result_Helper.java +++ b/src/vamsas/objects/simple/Result_Helper.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class Result_Helper { @@ -82,10 +101,10 @@ public class Result_Helper { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -94,10 +113,10 @@ public class Result_Helper { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/vamsas/objects/simple/Sequence.java b/src/vamsas/objects/simple/Sequence.java index d2eccb0..c8dd81e 100755 --- a/src/vamsas/objects/simple/Sequence.java +++ b/src/vamsas/objects/simple/Sequence.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class Sequence implements java.io.Serializable { @@ -24,7 +43,7 @@ public class Sequence implements java.io.Serializable { /** * Gets the id value for this Sequence. - * + * * @return id */ public java.lang.String getId() { @@ -34,7 +53,7 @@ public class Sequence implements java.io.Serializable { /** * Sets the id value for this Sequence. - * + * * @param id */ public void setId(java.lang.String id) { @@ -44,7 +63,7 @@ public class Sequence implements java.io.Serializable { /** * Gets the seq value for this Sequence. - * + * * @return seq */ public java.lang.String getSeq() { @@ -54,7 +73,7 @@ public class Sequence implements java.io.Serializable { /** * Sets the seq value for this Sequence. - * + * * @param seq */ public void setSeq(java.lang.String seq) { @@ -72,11 +91,11 @@ public class Sequence implements java.io.Serializable { } __equalsCalc = obj; boolean _equals; - _equals = true && - ((this.id==null && other.getId()==null) || + _equals = true && + ((this.id==null && other.getId()==null) || (this.id!=null && this.id.equals(other.getId()))) && - ((this.seq==null && other.getSeq()==null) || + ((this.seq==null && other.getSeq()==null) || (this.seq!=null && this.seq.equals(other.getSeq()))); __equalsCalc = null; diff --git a/src/vamsas/objects/simple/SequenceSet.java b/src/vamsas/objects/simple/SequenceSet.java index 62e58b4..f7fc39e 100755 --- a/src/vamsas/objects/simple/SequenceSet.java +++ b/src/vamsas/objects/simple/SequenceSet.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class SequenceSet implements java.io.Serializable { @@ -21,7 +40,7 @@ public class SequenceSet implements java.io.Serializable { /** * Gets the seqs value for this SequenceSet. - * + * * @return seqs */ public vamsas.objects.simple.Sequence[] getSeqs() { @@ -31,7 +50,7 @@ public class SequenceSet implements java.io.Serializable { /** * Sets the seqs value for this SequenceSet. - * + * * @param seqs */ public void setSeqs(vamsas.objects.simple.Sequence[] seqs) { @@ -49,8 +68,8 @@ public class SequenceSet implements java.io.Serializable { } __equalsCalc = obj; boolean _equals; - _equals = true && - ((this.seqs==null && other.getSeqs()==null) || + _equals = true && + ((this.seqs==null && other.getSeqs()==null) || (this.seqs!=null && java.util.Arrays.equals(this.seqs, other.getSeqs()))); __equalsCalc = null; diff --git a/src/vamsas/objects/simple/SequenceSet_Helper.java b/src/vamsas/objects/simple/SequenceSet_Helper.java index 77586ba..d5f04a0 100755 --- a/src/vamsas/objects/simple/SequenceSet_Helper.java +++ b/src/vamsas/objects/simple/SequenceSet_Helper.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class SequenceSet_Helper { @@ -32,10 +51,10 @@ public class SequenceSet_Helper { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -44,10 +63,10 @@ public class SequenceSet_Helper { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/vamsas/objects/simple/Sequence_Helper.java b/src/vamsas/objects/simple/Sequence_Helper.java index f675384..c8118c4 100755 --- a/src/vamsas/objects/simple/Sequence_Helper.java +++ b/src/vamsas/objects/simple/Sequence_Helper.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class Sequence_Helper { @@ -37,10 +56,10 @@ public class Sequence_Helper { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -49,10 +68,10 @@ public class Sequence_Helper { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } diff --git a/src/vamsas/objects/simple/WsJobId.java b/src/vamsas/objects/simple/WsJobId.java index 4bc1f2e..891201f 100755 --- a/src/vamsas/objects/simple/WsJobId.java +++ b/src/vamsas/objects/simple/WsJobId.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class WsJobId implements java.io.Serializable { @@ -24,7 +43,7 @@ public class WsJobId implements java.io.Serializable { /** * Gets the jobId value for this WsJobId. - * + * * @return jobId */ public java.lang.String getJobId() { @@ -34,7 +53,7 @@ public class WsJobId implements java.io.Serializable { /** * Sets the jobId value for this WsJobId. - * + * * @param jobId */ public void setJobId(java.lang.String jobId) { @@ -44,7 +63,7 @@ public class WsJobId implements java.io.Serializable { /** * Gets the status value for this WsJobId. - * + * * @return status */ public int getStatus() { @@ -54,7 +73,7 @@ public class WsJobId implements java.io.Serializable { /** * Sets the status value for this WsJobId. - * + * * @param status */ public void setStatus(int status) { @@ -72,8 +91,8 @@ public class WsJobId implements java.io.Serializable { } __equalsCalc = obj; boolean _equals; - _equals = true && - ((this.jobId==null && other.getJobId()==null) || + _equals = true && + ((this.jobId==null && other.getJobId()==null) || (this.jobId!=null && this.jobId.equals(other.getJobId()))) && this.status == other.getStatus(); diff --git a/src/vamsas/objects/simple/WsJobId_Helper.java b/src/vamsas/objects/simple/WsJobId_Helper.java index 3988ce9..042a32e 100755 --- a/src/vamsas/objects/simple/WsJobId_Helper.java +++ b/src/vamsas/objects/simple/WsJobId_Helper.java @@ -5,6 +5,25 @@ * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + package vamsas.objects.simple; public class WsJobId_Helper { @@ -37,10 +56,10 @@ public class WsJobId_Helper { * Get Custom Serializer */ public static org.apache.axis.encoding.Serializer getSerializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanSerializer( _javaType, _xmlType, typeDesc); } @@ -49,10 +68,10 @@ public class WsJobId_Helper { * Get Custom Deserializer */ public static org.apache.axis.encoding.Deserializer getDeserializer( - java.lang.String mechType, - java.lang.Class _javaType, + java.lang.String mechType, + java.lang.Class _javaType, javax.xml.namespace.QName _xmlType) { - return + return new org.apache.axis.encoding.ser.BeanDeserializer( _javaType, _xmlType, typeDesc); } -- 1.7.10.2