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Viewing changes to clustalW/tree/ClusterTreeOutput.h

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy, Steffen Moeller, Charles Plessy
  • Date: 2009-10-21 13:25:44 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20091021132544-r4hbcnjxp354wxh0
Tags: 2.0.12-1
https://launchpad.net/bugs/423648
https://launchpad.net/bugs/393769
http://bugs.debian.org/550893
* New upstream release (LP: #423648, #393769):
  - Uses Qt instead of lesstif.
  - Includes new code for UPGMA guide trees.
  - Includes iterative alignment facility.

[ Steffen Moeller ]
* New upstream release.
* Updated watch file (Closes: #550893).
* Removed LICENSE from debian/clustalx.docs
* rename to clustalx seems no longer required in debian/rules
* moved clustalx.1 into debian folder (eases working with svn-buildpackage)
* added German translation to desktop file

[ Charles Plessy ]
* Updated my email address.
* debian/copyright made machine-readable.
* Added various informations in debian/upstream-metadata.yaml.
* Switched to Debhelper 7.
  (debian/rules, debian/control, debian/patches, debian/compat)
* Removed useless Debhelper file debian/clustalx.dirs.
* Updated package description.
* Hardcoded the localisation of accessory files in /usr/share/clustalx.
  (debian/patches/hardcode-accessory-file-locations.patch)
* Documented in debian/README.source that the documentation for quilt
  is in /usr/share/doc/quilt.
* Added upstream changelog downloaded from upstream website
  (debian/rules, debian/CHANGELOG.upstream).
* Incremented Standards-Version to reflect conformance with Policy 3.8.3
  (debian/control, no other changes needed).
* Updated homepage in debian/clustalw.1.

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clustalW/tree/ClusterTreeOutput.h
 
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/**
 
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 * Author: Mark Larkin
 
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 * 
 
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 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
 
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 */
 
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#ifndef CLUSTERTREEOUTPUT_H
 
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#define CLUSTERTREEOUTPUT_H
 
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#include <memory>
 
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#include <fstream>
 
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#include "../alignment/Alignment.h"
 
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#include "../general/clustalw.h"
 
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namespace clustalw
 
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{
 
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class ClusterTreeOutput
 
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{
 
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    public:
 
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        ClusterTreeOutput(clustalw::SeqInfo* seqInfo, int boot);
 
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        void printNexusTree(clustalw::PhyloTree* phyloTree, ofstream* tree,
 
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                   clustalw::Alignment *alignPtr, clustalw::DistMatrix* distMat, vector<int>* bootTotals);
 
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        void printTree(clustalw::PhyloTree* phyloTree, ofstream* tree, vector<int>* totals);
 
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        void printPhylipTree(clustalw::PhyloTree* phyloTree, ofstream* tree,
 
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                   clustalw::Alignment *alignPtr, clustalw::DistMatrix* distMat, vector<int>* bootTotals);
 
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        void printTreeDesc(clustalw::PhyloTree* phyloTree);
 
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    private:
 
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        ClusterTreeOutput(); // Dont allow contruction with default!!!!
 
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        int twoWaySplit(clustalw::PhyloTree* phyloTree, ofstream* tree, int startRow, 
 
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                    int flag, clustalw::Alignment *alignPtr, vector<int>* bootTotals);
 
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        int twoWaySplitNexus(clustalw::PhyloTree* phyloTree, ofstream* tree, int startRow,
 
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                    int flag, clustalw::Alignment *alignPtr, vector<int>* bootTotals);
 
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        /* Attributes! */
 
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        int firstSeq;
 
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        int lastSeq;
 
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        int numSeqs;
 
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        int bootstrap;
 
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};
 
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}
 
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#endif