Matlab cannot see some of my java classes (not all) in jar package

Question

I have a problem that is driving me nuts. Matlab sees only some of my classes embeded in a JAR file

If I compile the classes outside of a package and add the path to the class in Matlab using javaaddpath, I do not encounter any problem

When I compile the class in a package and then try to access them under Matlab, I have problems. Below some Matlab code

>>javaaddpath('/Users/me/Documents/workspace/EKGTest.jar');
>>clear java
>>import com.neurosky.thinkgear.*
>>methods('EkgSense')

Methods for class com.neurosky.thinkgear.EkgSense:

EkgSense                  getClass                  notify                    reset            
addTemplate               getClassificationResults  notifyAll                  toString
equals                    hashCode                  processData               wait   

>>methods('EkgEpoch')

No methods for class EkgEpoch or no class EkgEpoch

Now, I look in the package, all of the classes are public. This is a result of jar -tf

osx:/Users/me/Documents/workspace> jar tf EKGTest.jar
META-INF/MANIFEST.MF
META-INF/REFACTORINGS.XML
com/
com/neurosky/
com/neurosky/thinkgear/
com/neurosky/thinkgear/EkgEpoch.class
com/neurosky/thinkgear/EkgEpoch.java
com/neurosky/thinkgear/EkgParameters.class
com/neurosky/thinkgear/EkgParameters.java
com/neurosky/thinkgear/EkgTemplate.class
com/neurosky/thinkgear/EkgTemplate.java
com/neurosky/thinkgear/Matlab.class
com/neurosky/thinkgear/Matlab.java
com/neurosky/thinkgear/EkgSense.class
com/neurosky/thinkgear/EkgSense.java
com/neurosky/thinkgear/DistanceArray.class
com/neurosky/thinkgear/DistanceArray.java

and below of javap --classpath

osx:/Users/me/Documents/workspace> javap -classpath /Users/me/Documents/workspace/EKGTest.jar    com.neurosky.thinkgear.EkgEpoch
Compiled from "EkgEpoch.java"
public class com.neurosky.thinkgear.EkgEpoch extends java.lang.Object implements java.lang.Cloneable{
    public int numberOfSamples;
    public float[] data;
    public com.neurosky.thinkgear.EkgEpoch(int);
    public com.neurosky.thinkgear.EkgEpoch(int, float[]);
    public com.neurosky.thinkgear.EkgEpoch(float[]);
    public com.neurosky.thinkgear.EkgEpoch(com.neurosky.thinkgear.EkgEpoch);
    public com.neurosky.thinkgear.EkgEpoch(org.json.JSONArray);
    public org.json.JSONArray toJSONArray();
    public static float[] convolve(float[], float[]);
    public float getLineNoiseAmplitude();
    public com.neurosky.thinkgear.EkgEpoch subtract(com.neurosky.thinkgear.EkgEpoch);
    public com.neurosky.thinkgear.EkgEpoch subEpoch(int, int);
    public com.neurosky.thinkgear.EkgEpoch square();
    public com.neurosky.thinkgear.EkgEpoch subtract(float);
    public com.neurosky.thinkgear.EkgEpoch diff();
    public boolean exceedValue(float, int, int);
    public com.neurosky.thinkgear.EkgEpoch smooth(int);
    public float mean();
    public float sum();
    public float max();
    public float median();
    public com.neurosky.thinkgear.EkgEpoch clone();
    public com.neurosky.thinkgear.EkgEpoch sort();
    public int[] sortIndices(com.neurosky.thinkgear.EkgEpoch);
    public float std();
    public int find_heart_beats(int[], float);
    public com.neurosky.thinkgear.EkgEpoch detrend();
    public java.lang.Object clone()       throws java.lang.CloneNotSupportedException;
}

osx:/Users/me/Documents/workspace> javap -classpath /Users/me/Documents/workspace/EKGTest.jar  com.neurosky.thinkgear.EkgSense
Compiled from "EkgSense.java"
public class com.neurosky.thinkgear.EkgSense extends java.lang.Object{
    public com.neurosky.thinkgear.EkgParameters params;
    public com.neurosky.thinkgear.EkgTemplate[] templates;
    public com.neurosky.thinkgear.EkgTemplate currentData;
    public int lastTemplateInd;
    public float lastEpochValue;
    public com.neurosky.thinkgear.EkgSense(com.neurosky.thinkgear.EkgParameters);
    public void reset();
    public void addTemplate(java.lang.String, float[][]);
    public void addTemplate(com.neurosky.thinkgear.EkgTemplate);
    public java.lang.String getClassificationResults();
    public boolean processData(float[]);
}

I am running Matlab on OSX. I have tried with Matlab 7.7.0.471 (R2008b) and 7.11.0.584 (R2010b) and got the same problem. Both Matlab are using the native OSX Java (Java 1.6.0_26-b03-384-10M3425 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode) which should be the same as the one in Eclipse (I have checked and Eclipse compiles with 1.6).

Remember that I can see the missing class no problem when I remove the package statement and some imports at the top of the java files (in all the classes of course) and when I simply add the path to the .class files (not access them in a JAR file).

Any help would be greatly appreciated. Thanks,

Jason

Answer 1

I eventually found the problem which cannot be seen above. The problem (not documented anywhere) was that some of my classes use external packages that I had not imported into Matlab. I was not planning on using any of the functionalities linked with these packages.

Nevertheless, the Matlab error message that it cannot find the class is puzzling. An error message indicating that the class cannot be used because some packages are not referenced would be most useful.

If your package uses external packages, make sure to include all of the relevant jar files in the java classpath or Matlab will not see your dependent classes.

Another tip that I found useful is that the Matlab function "import" will not return an error if you enter a package that does not exist, e.g., import java.doesnotexist.* works fine. However, import java.doesnotexist.aclass will not work.

Jason