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Viewing changes to src/main/org/openscience/cdk/AtomContainerSet.java

  • Committer: Bazaar Package Importer
  • Author(s): Onkar Shinde
  • Date: 2011-05-30 20:50:41 UTC
  • mfrom: (1.1.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20110530205041-78aklnmmeg2nal1s
Tags: 1:1.2.10-1
http://bugs.debian.org/627582
http://bugs.debian.org/627712
http://bugs.debian.org/627683
* New upstream release. (Closes: #627582, #627712)
* debian/control
  - Drop bunch of not used build dependencies - libcommons-cli-java,
    libcrimson-java, libmysql-java, libpgjava, xsltproc.
  - Add javahelper as build dependency to use jh_classpath and jh_depends
    utilities.
* debian/rules
  - Include javahelper.mk
  - Remove ant-nodeps, vecmath, log4j-1.2, commons-cli from build classpath.
    Build classpath is managed by upstream build system.
  - Remove modules which do not contain any class files when built - inchi,
    pdbcml, qsarxml.
  - Add logic to generate debian/classpath file. This file is used by
    jh_classpath to update classpath in manifest files. (Closes: #627683)
* debian/patches/
  - 21_vecmath_lib_name.patch - Remove. Not needed anymore.
  - 22_fix_build.patch - Update as per current upstream source.

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src/main/org/openscience/cdk/AtomContainerSet.java
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        /**  Constructs an empty AtomContainerSet. */
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        public AtomContainerSet() {
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                atomContainerCount = 0;
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                atomContainers = new AtomContainer[growArraySize];
 
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                atomContainers = new IAtomContainer[growArraySize];
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                multipliers = new Double[growArraySize];
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        }
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         */
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        protected void growAtomContainerArray() {
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                growArraySize = atomContainers.length;
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                AtomContainer[] newatomContainers = new AtomContainer[atomContainers.length + growArraySize];
 
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                IAtomContainer[] newatomContainers = new IAtomContainer[atomContainers.length + growArraySize];
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                System.arraycopy(atomContainers, 0, newatomContainers, 0, atomContainers.length);
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                atomContainers = newatomContainers;
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                Double[] newMultipliers = new Double[multipliers.length + growArraySize];
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         */
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        public Object clone() throws CloneNotSupportedException {
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                AtomContainerSet clone = (AtomContainerSet)super.clone();
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                clone.atomContainers = new AtomContainer[atomContainerCount];
 
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                clone.atomContainers = new IAtomContainer[atomContainerCount];
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                clone.atomContainerCount = 0;
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                for (int i = 0; i < atomContainerCount; i++) {
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                    clone.addAtomContainer((IAtomContainer)atomContainers[i].clone());