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Use var name idx 0 .. n instead of number 1 .. n. Also update documen…
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…tation to reflect an exception should now be thrown on out of bounds.
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@johnmay
johnmay committed May 7, 2017
1 parent 3e54ffd commit 84130b4
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Showing 13 changed files with 152 additions and 144 deletions.
8 changes: 4 additions & 4 deletions base/core/src/main/java/org/openscience/cdk/graph/AllPairsShortestPaths.java
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Original file line number Diff line number Diff line change
Expand Up @@ -180,25 +180,25 @@ public void setBonds(IBond[] bonds) {}
public void setAtom(int number, IAtom atom) {}

@Override
public IAtom getAtom(int number) {
public IAtom getAtom(int idx) {
throw new UnsupportedOperationException(
"not supported");
}

@Override
public IBond getBond(int number) {
public IBond getBond(int idx) {
throw new UnsupportedOperationException(
"not supported");
}

@Override
public ILonePair getLonePair(int number) {
public ILonePair getLonePair(int idx) {
throw new UnsupportedOperationException(
"not supported");
}

@Override
public ISingleElectron getSingleElectron(int number) {
public ISingleElectron getSingleElectron(int idx) {
throw new UnsupportedOperationException(
"not supported");
}
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16 changes: 8 additions & 8 deletions base/data/src/main/java/org/openscience/cdk/AtomContainer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -311,32 +311,32 @@ public void setAtom(int idx, IAtom atom) {
* {@inheritDoc}
*/
@Override
public IAtom getAtom(int number) {
return atoms[number];
public IAtom getAtom(int idx) {
return atoms[idx];
}

/**
* {@inheritDoc}
*/
@Override
public IBond getBond(int number) {
return bonds[number];
public IBond getBond(int idx) {
return bonds[idx];
}

/**
* {@inheritDoc}
*/
@Override
public ILonePair getLonePair(int number) {
return lonePairs[number];
public ILonePair getLonePair(int idx) {
return lonePairs[idx];
}

/**
* {@inheritDoc}
*/
@Override
public ISingleElectron getSingleElectron(int number) {
return singleElectrons[number];
public ISingleElectron getSingleElectron(int idx) {
return singleElectrons[idx];
}

/**
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24 changes: 12 additions & 12 deletions base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAminoAcid.java
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Original file line number Diff line number Diff line change
Expand Up @@ -85,30 +85,30 @@ public void setAtom(int number, IAtom atom) {

/** {@inheritDoc} */
@Override
public IAtom getAtom(int number) {
logger.debug("Getting atom at: ", number);
return super.getAtom(number);
public IAtom getAtom(int idx) {
logger.debug("Getting atom at: ", idx);
return super.getAtom(idx);
}

/** {@inheritDoc} */
@Override
public IBond getBond(int number) {
logger.debug("Getting bond at: ", number);
return super.getBond(number);
public IBond getBond(int idx) {
logger.debug("Getting bond at: ", idx);
return super.getBond(idx);
}

/** {@inheritDoc} */
@Override
public ILonePair getLonePair(int number) {
logger.debug("Getting lone pair at: ", number);
return super.getLonePair(number);
public ILonePair getLonePair(int idx) {
logger.debug("Getting lone pair at: ", idx);
return super.getLonePair(idx);
}

/** {@inheritDoc} */
@Override
public ISingleElectron getSingleElectron(int number) {
logger.debug("Getting single electron at: ", number);
return super.getSingleElectron(number);
public ISingleElectron getSingleElectron(int idx) {
logger.debug("Getting single electron at: ", idx);
return super.getSingleElectron(idx);
}

// public void setElectronContainer(int number, IElectronContainer electronContainer) {
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24 changes: 12 additions & 12 deletions base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -111,36 +111,36 @@ public void setAtom(int number, IAtom atom) {
* {@inheritDoc}
*/
@Override
public IAtom getAtom(int number) {
logger.debug("Getting atom at: ", number);
return super.getAtom(number);
public IAtom getAtom(int idx) {
logger.debug("Getting atom at: ", idx);
return super.getAtom(idx);
}

/**
* {@inheritDoc}
*/
@Override
public IBond getBond(int number) {
logger.debug("Getting bond at: ", number);
return super.getBond(number);
public IBond getBond(int idx) {
logger.debug("Getting bond at: ", idx);
return super.getBond(idx);
}

/**
* {@inheritDoc}
*/
@Override
public ILonePair getLonePair(int number) {
logger.debug("Getting lone pair at: ", number);
return super.getLonePair(number);
public ILonePair getLonePair(int idx) {
logger.debug("Getting lone pair at: ", idx);
return super.getLonePair(idx);
}

/**
* {@inheritDoc}
*/
@Override
public ISingleElectron getSingleElectron(int number) {
logger.debug("Getting single electron at: ", number);
return super.getSingleElectron(number);
public ISingleElectron getSingleElectron(int idx) {
logger.debug("Getting single electron at: ", idx);
return super.getSingleElectron(idx);
}

/**
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24 changes: 12 additions & 12 deletions base/datadebug/src/main/java/org/openscience/cdk/debug/DebugBioPolymer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -88,30 +88,30 @@ public void setAtom(int number, IAtom atom) {

/** {@inheritDoc} */
@Override
public IAtom getAtom(int number) {
logger.debug("Getting atom at: ", number);
return super.getAtom(number);
public IAtom getAtom(int idx) {
logger.debug("Getting atom at: ", idx);
return super.getAtom(idx);
}

/** {@inheritDoc} */
@Override
public IBond getBond(int number) {
logger.debug("Getting bond at: ", number);
return super.getBond(number);
public IBond getBond(int idx) {
logger.debug("Getting bond at: ", idx);
return super.getBond(idx);
}

/** {@inheritDoc} */
@Override
public ILonePair getLonePair(int number) {
logger.debug("Getting lone pair at: ", number);
return super.getLonePair(number);
public ILonePair getLonePair(int idx) {
logger.debug("Getting lone pair at: ", idx);
return super.getLonePair(idx);
}

/** {@inheritDoc} */
@Override
public ISingleElectron getSingleElectron(int number) {
logger.debug("Getting single electron at: ", number);
return super.getSingleElectron(number);
public ISingleElectron getSingleElectron(int idx) {
logger.debug("Getting single electron at: ", idx);
return super.getSingleElectron(idx);
}

// public void setElectronContainer(int number, IElectronContainer electronContainer) {
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24 changes: 12 additions & 12 deletions base/datadebug/src/main/java/org/openscience/cdk/debug/DebugCrystal.java
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Original file line number Diff line number Diff line change
Expand Up @@ -95,30 +95,30 @@ public void setAtom(int number, IAtom atom) {

/** {@inheritDoc} */
@Override
public IAtom getAtom(int number) {
logger.debug("Getting atom at: ", number);
return super.getAtom(number);
public IAtom getAtom(int idx) {
logger.debug("Getting atom at: ", idx);
return super.getAtom(idx);
}

/** {@inheritDoc} */
@Override
public IBond getBond(int number) {
logger.debug("Getting bond at: ", number);
return super.getBond(number);
public IBond getBond(int idx) {
logger.debug("Getting bond at: ", idx);
return super.getBond(idx);
}

/** {@inheritDoc} */
@Override
public ILonePair getLonePair(int number) {
logger.debug("Getting lone pair at: ", number);
return super.getLonePair(number);
public ILonePair getLonePair(int idx) {
logger.debug("Getting lone pair at: ", idx);
return super.getLonePair(idx);
}

/** {@inheritDoc} */
@Override
public ISingleElectron getSingleElectron(int number) {
logger.debug("Getting single electron at: ", number);
return super.getSingleElectron(number);
public ISingleElectron getSingleElectron(int idx) {
logger.debug("Getting single electron at: ", idx);
return super.getSingleElectron(idx);
}

// public void setElectronContainer(int number, IElectronContainer electronContainer) {
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24 changes: 12 additions & 12 deletions base/datadebug/src/main/java/org/openscience/cdk/debug/DebugMonomer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -85,30 +85,30 @@ public void setAtom(int number, IAtom atom) {

/** {@inheritDoc} */
@Override
public IAtom getAtom(int number) {
logger.debug("Getting atom at: ", number);
return super.getAtom(number);
public IAtom getAtom(int idx) {
logger.debug("Getting atom at: ", idx);
return super.getAtom(idx);
}

/** {@inheritDoc} */
@Override
public IBond getBond(int number) {
logger.debug("Getting bond at: ", number);
return super.getBond(number);
public IBond getBond(int idx) {
logger.debug("Getting bond at: ", idx);
return super.getBond(idx);
}

/** {@inheritDoc} */
@Override
public ILonePair getLonePair(int number) {
logger.debug("Getting lone pair at: ", number);
return super.getLonePair(number);
public ILonePair getLonePair(int idx) {
logger.debug("Getting lone pair at: ", idx);
return super.getLonePair(idx);
}

/** {@inheritDoc} */
@Override
public ISingleElectron getSingleElectron(int number) {
logger.debug("Getting single electron at: ", number);
return super.getSingleElectron(number);
public ISingleElectron getSingleElectron(int idx) {
logger.debug("Getting single electron at: ", idx);
return super.getSingleElectron(idx);
}

// public void setElectronContainer(int number, IElectronContainer electronContainer) {
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24 changes: 12 additions & 12 deletions base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPolymer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -87,30 +87,30 @@ public void setAtom(int number, IAtom atom) {

/** {@inheritDoc} */
@Override
public IAtom getAtom(int number) {
logger.debug("Getting atom at: ", number);
return super.getAtom(number);
public IAtom getAtom(int idx) {
logger.debug("Getting atom at: ", idx);
return super.getAtom(idx);
}

/** {@inheritDoc} */
@Override
public IBond getBond(int number) {
logger.debug("Getting bond at: ", number);
return super.getBond(number);
public IBond getBond(int idx) {
logger.debug("Getting bond at: ", idx);
return super.getBond(idx);
}

/** {@inheritDoc} */
@Override
public ILonePair getLonePair(int number) {
logger.debug("Getting lone pair at: ", number);
return super.getLonePair(number);
public ILonePair getLonePair(int idx) {
logger.debug("Getting lone pair at: ", idx);
return super.getLonePair(idx);
}

/** {@inheritDoc} */
@Override
public ISingleElectron getSingleElectron(int number) {
logger.debug("Getting single electron at: ", number);
return super.getSingleElectron(number);
public ISingleElectron getSingleElectron(int idx) {
logger.debug("Getting single electron at: ", idx);
return super.getSingleElectron(idx);
}

// public void setElectronContainer(int number, IElectronContainer electronContainer) {
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24 changes: 12 additions & 12 deletions base/datadebug/src/main/java/org/openscience/cdk/debug/DebugRing.java
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Original file line number Diff line number Diff line change
Expand Up @@ -110,30 +110,30 @@ public void setAtom(int number, IAtom atom) {

/** {@inheritDoc} */
@Override
public IAtom getAtom(int number) {
logger.debug("Getting atom at: ", number);
return super.getAtom(number);
public IAtom getAtom(int idx) {
logger.debug("Getting atom at: ", idx);
return super.getAtom(idx);
}

/** {@inheritDoc} */
@Override
public IBond getBond(int number) {
logger.debug("Getting bond at: ", number);
return super.getBond(number);
public IBond getBond(int idx) {
logger.debug("Getting bond at: ", idx);
return super.getBond(idx);
}

/** {@inheritDoc} */
@Override
public ILonePair getLonePair(int number) {
logger.debug("Getting lone pair at: ", number);
return super.getLonePair(number);
public ILonePair getLonePair(int idx) {
logger.debug("Getting lone pair at: ", idx);
return super.getLonePair(idx);
}

/** {@inheritDoc} */
@Override
public ISingleElectron getSingleElectron(int number) {
logger.debug("Getting single electron at: ", number);
return super.getSingleElectron(number);
public ISingleElectron getSingleElectron(int idx) {
logger.debug("Getting single electron at: ", idx);
return super.getSingleElectron(idx);
}

// public void setElectronContainer(int number, IElectronContainer electronContainer) {
Expand Down
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